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Clinical effect of local pretreatment with dexamethasone on lower back pain after epidural labor analgesia	This report aims to retrospectively analyze the clinical effect of local pretreatment with dexamethasone (DXMS) on lower back pain after epidural labor analgesia. Patients with epidural labor analgesia treated in People's Hospital of Rizhao from January 2014 to December 2016 were studied. All 368 cases involved were pregnant primipara with full-term single birth. Parturient received injection of DXMS and lidocaine mixture around the epidural puncture point was the observation group (n=188), and parturient received injection of 0.9% sodium chloride and lidocaine mixture around the epidural puncture point was the control group (n=180). The incidence and degree of lower back pain postoperatively in the two groups were evaluated by pain visual analogue scale method. The incidence of lower back pain at 48 h, 72 h after operation in observation group was significantly lower than that in control group (p<0.05). Among patients undergoing one puncture and more than one puncture, the incidence of postoperative lower back pain in the observation group was significantly lower than that in the control group (59.26%) (p<0.05). Among the parturient with spontaneous delivery, the incidence of postoperative lower back pain in the observation group was significantly lower than that in the control group (p=0.028). Among the cesarean section patients, the incidence of pain in observation group was significantly lower than that in control group (p=0.019). At 48 and 72 h after operation, severe pain in the observation group was significantly less than that in the control group (p<0.05). DXMS local pretreatment can significantly reduce the incidence of postoperative lower back pain and the degree of pain after epidural delivery analgesia. DXMS pretreatment in epidural analgesia deserved to be widely used clinically.	[ "Epidural corticosteroid injections are a common treatment for radicular pain caused by intervertebral disc herniations, spinal stenosis, and other disorders. Although rare, catastrophic neurologic injuries, including stroke and spinal cord injury, have occurred with these injections. A collaboration was undertaken between the U.S. Food and Drug Administration Safe Use Initiative, an expert multidisciplinary working group, and 13 specialty stakeholder societies. The goal of this collaboration was to review the existing evidence regarding neurologic complications associated with epidural corticosteroid injections and produce consensus procedural clinical considerations aimed at enhancing the safety of these injections. U.S. Food and Drug Administration Safe Use Initiative representatives helped convene and facilitate meetings without actively participating in the deliberations or decision-making process. Seventeen clinical considerations aimed at improving safety were produced by the stakeholder societies. Specific clinical considerations for performing transforaminal and interlaminar injections, including the use of nonparticulate steroid, anatomic considerations, and use of radiographic guidance are given along with the existing scientific evidence for each clinical consideration. Adherence to specific recommended practices when performing epidural corticosteroid injections should lead to a reduction in the incidence of neurologic injuries.", "Regional analgesia is commonly used for the relief of labour pain, Prolongation of analgesia can be achieved by adjuvant medications. The aim of this randomised controlled trial was to evaluate the efficacy of intrathecal levobupivacaine with dexamethasone for labour analgesia. A total of 80 females were included in this study, all were primigravidas undergoing vaginal delivery with cervical dilatation ≥4 cm and 50% or more effacement. Forty females were included randomly in either Group L (received intrathecal levobupivacaine 0.25% in 2 mL) or Group LD (received intrathecal levobupivacaine 0.25% combined with dexamethasone 4 mg in 2 mL). The primary outcome was the duration of spinal analgesia. Secondary outcomes included the total dose of epidural local anaesthetic given, time to delivery, neonatal outcome and adverse effects. The duration of spinal analgesia was significantly longer in the LD group compared with L group (80.5 ± 12.4 min vs. 57.1 ± 11.5 min, respectively; P < 0.001). In Group LD compared with Group L, time from spinal analgesia to delivery was significantly lower (317.4 ± 98.9 min vs. 372.4 ± 118.8 min, respectively; P = 0.027), and total epidural levobupivacaine consumption was significantly lower (102.4 ± 34.8 mg vs. 120.1 ± 41.9 mg, respectively; P = 0.027). The two groups were comparable with respect to characteristics of sensory and motor block, haemodynamic parameters, pain scores, neonatal outcome and frequency of adverse effects. Intrathecal dexamethasone plus levobupivacaine prolongs the duration of spinal analgesia during combined spinal-epidural CSE for labour analgesia.", "In this study, we sought to determine the frequency and outcomes of epidural hematomas after epidural catheterization. Eleven centers participating in the Multicenter Perioperative Outcomes Group used electronic anesthesia information systems and quality assurance databases to identify patients who had epidural catheters inserted for either obstetrical or surgical indications. From this cohort, patients undergoing laminectomy for the evacuation of hematoma within 6 weeks of epidural placement were identified. Seven of 62,450 patients undergoing perioperative epidural catheterizations developed hematoma requiring surgical evacuation. The event rate was 11.2 × 10(-5) (95% confidence interval [CI], 4.5 × 10(-5) to 23.1 × 10(-5)). Four of the 7 had anticoagulation/antiplatelet therapy that deviated from American Society of Regional Anesthesia guidelines. None of 79,837 obstetric patients with epidural catheterizations developed hematoma (upper limit of the 95% CI, 4.6 × 10(-5)). The hematoma rate in obstetric epidural catheterizations was significantly lower than in perioperative epidural catheterizations (P = 0.003). In this series, the 95% CI for the frequency of epidural hematoma requiring laminectomy after epidural catheter placement for perioperative anesthesia/analgesia was 1 event per 22,189 placements to 1 event per 4330 placements. Risk was significantly lower in obstetric epidurals.", "Nonsteroidal anti-inflammatory drugs (NSAIDs) are frequently used for postoperative pain control. However, concerns regarding the potential deleterious effects of NSAIDs on bone healing have compelled many physicians to avoid NSAIDs in patients with healing fractures, osteotomies, and fusions. We systematically reviewed and analyzed the best clinical evidence regarding the effects of NSAID exposure on bone healing. Medline, Embase, and Cochrane electronic databases were searched for prospective and retrospective clinical studies of fracture, osteotomy, and fusion studies of patients with NSAID exposure and nonunion as an outcome. Study quality was assessed using the Newcastle-Ottawa Scale. Data on study design, patient characteristics, and risk estimates were extracted. Pooled effect estimates were calculated. Subanalyses were performed by bone type and by NSAID dose, duration, and route of administration. In the initial analysis of 11 cohort and case-control studies, the pooled odds ratio for nonunion with NSAID exposure was 3.0 (95% confidence interval 1.6-5.6). A significant association between lower-quality studies and higher reported odds ratios for nonunion was observed. When only higher-quality studies were considered, seven spine fusion studies were analyzed, and no statistically significant association between NSAID exposure and nonunion was identified (odds ratio = 2.2, 95% confidence interval 0.8-6.3). There was no increased risk of nonunion with NSAID exposure when only the highest-quality studies were assessed. Randomized controlled trials assessing NSAID exposure in fracture, fusion, and osteotomy populations are warranted to confirm or refute the findings of this meta-analysis of observational studies.", "Major spine surgery with multilevel instrumentation is followed by large amount of opioid consumption, significant pain and difficult mobilization in a population of predominantly chronic pain patients. This case-control study investigated if a standardized comprehensive pain and postoperative nausea and vomiting (PONV) treatment protocol would improve pain treatment in this population. A new regimen with acetaminophen, NSAIDs, gabapentin, S-ketamine, dexamethasone, ondansetron and epidural local anesthetic infusion or patient controlled analgesia with morphine, was introduced in a post-intervention group of 41 consecutive patients undergoing multilevel (median 10) instrumented spinal fusions and compared with 44 patients in a pre-intervention group. Compared to patients in the pre-intervention group, patients treated according to the new protocol consumed less opioid on postoperative day (POD) 1 (P = 0.024) and 2 (P = 0.048), they were mobilized earlier from bed (P = 0.003) and ambulation was earlier both with and without a walking frame (P = 0.027 and P = 0.027, respectively). Finally, patients following the new protocol experienced low intensities of nausea, sedation and dizziness on POD 1-6. In this study of patients scheduled for multilevel spine surgery, it was demonstrated that compared to a historic group of patients receiving usual care, a comprehensive and standardized multimodal pain and PONV protocol significantly reduced opioid consumption, improved postoperative mobilization and presented concomitant low levels of nausea, sedation and dizziness.", "Acupuncture is commonly used as a complimentary treatment for pain management. However, there has been no systematic review summarizing the current evidence concerning the effectiveness of acupuncture for acute postoperative pain after back surgery. This systematic review aimed at evaluating the effectiveness of acupuncture treatment for acute postoperative pain (≤1 week) after back surgery. We searched 15 electronic databases without language restrictions. Two reviewers independently assessed studies for eligibility and extracted data, outcomes, and risk of bias. Random effect meta-analyses and subgroup analyses were performed. Five trials, including 3 of high quality, met our inclusion criteria. The meta-analysis showed positive results for acupuncture treatment of pain after surgery in terms of the visual analogue scale (VAS) for pain intensity 24 hours after surgery, when compared to sham acupuncture (standard mean difference -0.67 (-1.04 to -0.31), P = 0.0003), whereas the other meta-analysis did not show a positive effect of acupuncture on 24-hour opiate demands when compared to sham acupuncture (standard mean difference -0.23 (-0.58 to 0.13), P = 0.21). Our systematic review finds encouraging but limited evidence for the effectiveness of acupuncture treatment for acute postoperative pain after back surgery. Further rigorously designed clinical trials are required.", "Patients undergoing complex spine surgery frequently experience severe pain in the postoperative period. The combined opiate receptor agonist/N-methyl-d-aspartate receptor antagonist methadone may be an optimal drug for these patients given the probable involvement of N-methyl-d-aspartate systems in the mechanism of opioid tolerance and hyperalgesia. Twenty-nine patients undergoing multilevel thoracolumbar spine surgery with instrumentation and fusion were enrolled in this prospective study and randomized to receive either methadone (0.2 mg/kg) before surgical incision or a continuous sufentanil infusion of 0.25 μg/kg/h after a load of 0.75 μg/kg. Postoperative analgesia was provided using IV opioids by patient-controlled analgesia. Patients were assessed with respect to pain scores (visual analog scale from 0 to 10), cumulative opioid requirement, and side effects at 24, 48, and 72 hours after surgery. Demographic data, duration, and type of surgery were comparable between the groups. Methadone reduced postoperative opioid requirement by approximately 50% at 48 hours (sufentanil versus methadone group, median [25%/75% interquartile range]: 63 mg [27.3/86.1] vs 25 mg [16.5/31.5] morphine equivalents, P = 0.023; and 72 hours: 34 mg [19.9/91.5] vs 15 mg [8.8/27.8] morphine equivalents, P = 0.024) after surgery. In addition, pain scores were lower by approximately 50% in the methadone group at 48 hours after surgery (sufentanil versus methadone group [mean ± SD] 4.8 ± 2.4 vs 2.8 ± 2.0, P = 0.026). The incidence of side effects was comparable in both groups. Perioperative treatment with a single bolus of methadone improves postoperative pain control for patients undergoing complex spine surgery." ]
Dendritic Cells as Vaccines in Cancer Immunotherapy	Dendritic cells (DCs) are recognized as highly potent antigen-presenting cells that are able to stimulate cytotoxic T lymphocyte (CTL) responses with antitumor activity. Consequently, DCs have been explored as cellular vaccines in cancer immunotherapy. To that end, DCs are modified with tumor antigens to enable presentation of antigen-derived peptides to CTLs. In this review we discuss the use of viral vectors for	[ "Activation of T cells requires at least two signals: an antigen-specific signal delivered through the T-cell receptor and a costimulatory signal mediated through molecules designated B7-1 and B7-2. Previous studies have shown that introduction of B7-1 and B7-2 into tumors using retroviral vectors has led to enhanced antitumor effects. A limiting factor for potential clinical applications using this approach is the low efficiency of infection of retroviral vectors and consequent manipulations of infected cells. Vaccinia virus thus represents an alternative vector for B7 gene expression in tumor cells. In this report we describe the construction and characterization of recombinant vaccinia viruses containing the murine B7-1 and B7-2 genes (designated rV-B7-1 and rV-B7-2). Infection of BSC-1 cells with these constructs results in rapid and efficient cell surface expression of both B7-1 and B7-2 (> 97% of cells at 4 h). Infection of murine carcinoma cells with low multiplicity of infection of wild-type vaccinia virus leads to the death of the host following tumor transplantation. In contrast, inoculation of rV-B7-1- or rV-B7-2-infected tumor cells into immunocompetent animals resulted in no tumor growth. These studies demonstrate the utility of recombinant vaccinia viruses to deliver B7 molecules to tumor cells for potential gene therapy and recombinant approaches to cancer immunotherapy.", "Ex vivo lentivirally transduced dendritic cells (DC) have been described to induce CD8+ and CD4+ T-cell responses against various tumor-associated antigens (TAAs) in vitro and in vivo. We report here that direct administration of ovalbumin (OVA) encoding lentiviral vectors caused in vivo transduction of cells that were found in draining lymph nodes (LNs) and induced potent anti-OVA cytotoxic T cells similar to those elicited by ex vivo transduced DC. The cytotoxic T-lymphocyte (CTL) response following direct injection of lentiviral vectors was highly effective in eliminating target cells in vivo up to 30 days after immunization and was efficiently recalled after a boost immunization. Injection of lentiviral vectors furthermore activated OVA-specific CD4+ T cells and this CD4 help was shown to be necessary for an adequate primary and memory CTL response. When tested in therapeutic tumor experiments with OVA+ melanoma cells, direct administration of lentiviral vectors slowed down tumor growth to a comparable extent with the highest dose of ex vivo transduced DC. Taken together, these data indicate that direct in vivo administration of lentiviral vectors encoding TAAs has strong potential for anticancer vaccination.", "The ability to target antigen-presenting cells with vectors encoding desired antigens holds the promise of potent prophylactic and therapeutic vaccines for infectious diseases and cancer. Toward this goal, we derived variants of the prototype alphavirus, Sindbis virus (SIN), with differential abilities to infect human dendritic cells. Cloning and sequencing of the SIN variant genomes revealed that the genetic determinant for human dendritic cell (DC) tropism mapped to a single amino acid substitution at residue 160 of the envelope glycoprotein E2. Packaging of SIN replicon vectors with the E2 glycoprotein from a DC-tropic variant conferred a similar ability to efficiently infect immature human DC, whereupon those DC were observed to undergo rapid activation and maturation. The SIN replicon particles infected skin-resident mouse DC in vivo, which subsequently migrated to the draining lymph nodes and upregulated cell surface expression of major histocompatibility complex and costimulatory molecules. Furthermore, SIN replicon particles encoding human immunodeficiency virus type 1 p55(Gag) elicited robust Gag-specific T-cell responses in vitro and in vivo, demonstrating that infected DC maintained their ability to process and present replicon-encoded antigen. Interestingly, human and mouse DC were differentially infected by selected SIN variants, suggesting differences in receptor expression between human and murine DC. Taken together, these data illustrate the tremendous potential of using a directed approach in generating alphavirus vaccine vectors that target and activate antigen-presenting cells, resulting in robust antigen-specific immune responses.", "Cancer vaccines targeting tumor-associated antigens are being investigated for the therapy of tumors. Numerous strategies, including the direct intratumoral (i.t.) vaccination route, have been examined. For tumors expressing carcinoembryonic antigen (CEA) as a model tumor-associated antigen, we previously designed poxviral vectors that contain the transgenes for CEA and a triad of T-cell costimulatory molecules, B7-1, intercellular adhesion molecule-1, (ICAM-1), and leukocyte function associated antigen-3 (LFA-3) (CEA/TRICOM). Two types of poxvirus vectors were developed: replication-competent recombinant vaccinia and replication-defective recombinant fowlpox. We have shown previously that a vaccine regimen composed of priming mice s.c. with recombinant vaccinia-CEA/TRICOM and boosting i.t. with recombinant fowlpox-CEA/TRICOM was superior to priming and boosting vaccinations using the conventional s.c. route in inducing T-cell responses specific for CEA. These studies also showed that CEA was needed to be present both in the vaccine and in the tumor for therapeutic effects. To determine specific immune responses associated with vaccination-mediated tumor regression, CEA-transgenic mice bearing CEA(+) tumors were vaccinated with the CEA/TRICOM s.c./i.t. regimen, and T-cell immune responses were assessed. In CEA(+) tumor-bearing mice vaccinated with the CEA/TRICOM s.c./i.t. regimen, T-cell responses could be detected not only to CEA encoded in vaccine vectors but also to other antigens expressed on the tumor itself: wild-type p53 and an endogenous retroviral epitope of gp70. Moreover, the magnitude of CD8(+) T-cell immune responses to gp70 was far greater than that induced to CEA or p53. Finally, the predominant T-cell population infiltrating the regressing CEA(+) tumor after therapy was specific for gp70. These studies show that the breadth and magnitude of antitumor immune cascades to multiple antigens could be critical in the therapy of established tumors.", "Using vaccinia virus as a live vector, we show that the expression of human papillomavirus type 16 (HPV-16) E7 fused to a nonhemolytic portion of the Listeria monocytogenes virulence factor, listeriolysin O (LLO), induces an immune response that causes the regression of established HPV-16 immortalized tumors in C57BL/6 mice. The vaccinia virus construct expressing LLO fused to E7 (VacLLOE7) was compared with two previously described vaccinia virus constructs: one that expresses unmodified E7 (VacE7) and another that expresses E7 in a form designed to direct it to intracellular lysosomal compartments and improve major histocompatibility complex class II-restricted responses (VacSigE7LAMP-1). C57BL/6 mice bearing established HPV-16 immortalized tumors of 5 or 8 mm were treated with each of these vaccines. Fifty percent of the mice treated with VacLLOE7 remained tumor free 2 months after tumor inoculation, whereas 12 to 25% of the mice were tumor free after treatment with VacSigE7LAMP-1 (depending on the size of the tumor). No mice were tumor free in the group given VacE7. Compared to VacE7, VacSigE7LAMP-1 and VacLLOE7 resulted in increased numbers of H2-D(b)-specific tetramer-positive CD8(+) T cells in mouse spleens that produced gamma interferon and tumor necrosis factor alpha upon stimulation with RAHYNIVTF peptide. In addition, the highest frequency of tetramer-positive T cells was seen in the tumor sites of mice treated with VacLLOE7. An increased efficiency of E7-specific lysis by splenocytes from mice immunized with VacLLOE7 was also observed. These results indicate that the fusion of E7 with LLO not only enhances antitumor therapy by improving the tumoricidal function of E7-specific CD8(+) T cells but may also increase the number of antigen-specific CD8(+) T cells in the tumor, the principle site of antigen expression.", "Successful immunotherapy of established tumors depends on overcoming the suppressive influence of the local tumor microenvironment. The direct injection of vaccinia virus expressing the B7.1 (CD80) costimulatory molecule into melanoma lesions resulted in local and systemic immunity with associated clinical responses. Therefore, we sought to evaluate the effects of a vaccinia virus expressing three costimulatory molecules, B7.1, ICAM-1, and LFA-3 (rV-TRICOM), in patients with metastatic melanoma. A standard dose escalation phase I clinical trial was performed. Thirteen patients were enrolled and 12 were available for follow-up. Local vaccination was feasible, with only low-grade injection site reactions associated with mild fatigue and myalgia reported. There was one occurrence of grade 1 vitiligo. Overall there was a 30.7% objective clinical response, with one patient achieving a complete response for more than 22 months. An inverse association was detected between anti-vaccinia antibody and anti-vaccinia T cell responses. Patients who failed to respond to vaccination but received high-dose interleukin-2 had a trend toward improved survival. Collectively, these results confirm the safety profile and feasibility of direct injection of vaccinia virus expressing multiple costimulatory molecules in patients with established tumors. Further clinical investigation is needed to better define the role of antigen, adjuvant cytokines, costimulation, and cross-presentation in the host immune response to local vaccination with vaccinia viruses expressing immunomodulatory molecules.", "Reports of vitiligo associated with metastases and rare cases of spontaneous regression of disease have fueled enthusiasm for immunologic approaches to the treatment of advanced melanoma. More recent strategies have focused on using antigen-presenting dendritic cells as vaccines. We observed 3 cases of leukoderma associated with a novel adenovirus-mediated gp100/MART-1-transduced dendritic cell (MART indicates melanoma antigen recognized by T cells). All 3 patients had advanced metastatic melanoma. Despite the development of this leukodermic response, all patients experienced disease progression while under treatment. We provide the initial evidence for effective induction of a leukodermic response with a gp100/MART-1-transduced dendritic cell vaccine.", "Alphaviruses are arthropod-borne viruses with wide species ranges and diverse tissue tropisms. The cell surface receptors which allow infection of so many different species and cell types are still incompletely characterized. We show here that the widely expressed glycosaminoglycan heparan sulfate can participate in the binding of Sindbis virus to cells. Enzymatic removal of heparan sulfate or the use of heparan sulfate-deficient cells led to a large reduction in virus binding. Sindbis virus bound to immobilized heparin, and this interaction was blocked by neutralizing antibodies against the viral E2 glycoprotein. Further experiments showed that a high degree of sulfation was critical for the ability of heparin to bind Sindbis virus. However, Sindbis virus was still able to infect and replicate on cells which were completely deficient in heparan sulfate, indicating that additional receptors must be involved. Cell surface binding of another alphavirus, Ross River virus, was found to be independent of heparan sulfate.", "Antigen-presenting cells are a heterogeneous group of cells that are characterized by their functional specialization. Consequently, targeting specific antigen-presenting cell subsets offers opportunities to induce distinct T cell responses. Here we report on the generation and use of nanobodies (Nbs) to target lentivectors specifically to human lymph node-resident myeloid dendritic cells, demonstrating that Nbs represent a powerful tool to redirect lentivectors to human antigen-presenting cell subsets.", "Purpose Many patients with high-risk non-muscle-invasive bladder cancer (NMIBC) are either refractory to bacillus Calmette-Guerin (BCG) treatment or may experience disease relapse. We assessed the efficacy and safety of recombinant adenovirus interferon alfa with Syn3 (rAd-IFNα/Syn3), a replication-deficient recombinant adenovirus gene transfer vector, for patients with high-grade (HG) BCG-refractory or relapsed NMIBC. Methods In this open-label, multicenter (n = 13), parallel-arm, phase II study ( ClinicalTrials.gov identifier: NCT01687244), 43 patients with HG BCG-refractory or relapsed NMIBC received intravesical rAd-IFNα/Syn3 (randomly assigned 1:1 to 1 × 1011 viral particles (vp)/mL or 3 × 1011 vp/mL). Patients who responded at months 3, 6, and 9 were retreated at months 4, 7, and 10. The primary end point was 12-month HG recurrence-free survival (RFS). All patients who received at least one dose were included in efficacy and safety analyses. Results Forty patients received rAd-IFNα/Syn3 (1 × 1011 vp/mL, n = 21; 3 × 1011 vp/mL, n = 19) between November 5, 2012, and April 8, 2015. Fourteen patients (35.0%; 90% CI, 22.6% to 49.2%) remained free of HG recurrence 12 months after initial treatment. Comparable 12-month HG RFS was noted for both doses. Of these 14 patients, two experienced recurrence at 21 and 28 months, respectively, after treatment initiation, and one died as a result of an upper tract tumor at 17 months without a recurrence. rAd-IFNα/Syn3 was well tolerated; no grade four or five adverse events (AEs) occurred, and no patient discontinued treatment because of an adverse event. The most frequently reported drug-related AEs were micturition urgency (n = 16; 40%), dysuria (n = 16; 40%), fatigue (n = 13; 32.5%), pollakiuria (n = 11; 28%), and hematuria and nocturia (n = 10 each; 25%). Conclusion rAd-IFNα/Syn3 was well tolerated. It demonstrated promising efficacy for patients with HG NMIBC after BCG therapy who were unable or unwilling to undergo radical cystectomy." ]
To study risk factors for decreasing a	To study risk factors for decreasing a	[ "Both amyloid-β (Aβ) deposition and brain atrophy are associated with Alzheimer's disease (AD) and the disease process likely begins many years before symptoms appear. We sought to determine whether clinically normal (CN) older individuals with Aβ deposition revealed by positron emission tomography (PET) imaging using Pittsburgh Compound B (PiB) also have evidence of both cortical thickness and hippocampal volume reductions in a pattern similar to that seen in AD. A total of 119 older individuals (87 CN subjects and 32 patients with mild AD) underwent PiB PET and high-resolution structural magnetic resonance imaging (MRI). Regression models were used to relate PiB retention to cortical thickness and hippocampal volume. We found that PiB retention in CN subjects was (1) age-related and (2) associated with cortical thickness reductions, particularly in parietal and posterior cingulate regions extending into the precuneus, in a pattern similar to that observed in mild AD. Hippocampal volume reduction was variably related to Aβ deposition. We conclude that Aβ deposition is associated with a pattern of cortical thickness reduction consistent with AD prior to the development of cognitive impairment.", "Cerebral accumulation of amyloid-β is thought to be the starting mechanism in Alzheimer's disease. Amyloid-β can be detected by analysis of cerebrospinal fluid amyloid-β42 or amyloid positron emission tomography, but it is unknown if any of the methods can identify an abnormal amyloid accumulation prior to the other. Our aim was to determine whether cerebrospinal fluid amyloid-β42 change before amyloid PET during preclinical stages of Alzheimer's disease. We included 437 non-demented subjects from the prospective, longitudinal Alzheimer's Disease Neuroimaging Initiative (ADNI) study. All underwent (18)F-florbetapir positron emission tomography and cerebrospinal fluid amyloid-β42 analysis at baseline and at least one additional positron emission tomography after a mean follow-up of 2.1 years (range 1.1-4.4 years). Group classifications were based on normal and abnormal cerebrospinal fluid and positron emission tomography results at baseline. We found that cases with isolated abnormal cerebrospinal fluid amyloid-β and normal positron emission tomography at baseline accumulated amyloid with a mean rate of 1.2%/year, which was similar to the rate in cases with both abnormal cerebrospinal fluid and positron emission tomography (1.2%/year, P = 0.86). The mean accumulation rate of those with isolated abnormal cerebrospinal fluid was more than three times that of those with both normal cerebrospinal fluid and positron emission tomography (0.35%/year, P = 0.018). The group differences were similar when analysing yearly change in standardized uptake value ratio of florbetapir instead of percentage change. Those with both abnormal cerebrospinal fluid and positron emission tomography deteriorated more in memory and hippocampal volume compared with the other groups (P < 0.001), indicating that they were closer to Alzheimer's disease dementia. The results were replicated after adjustments of different factors and when using different cut-offs for amyloid-β abnormality including a positron emission tomography classification based on the florbetapir uptake in regions where the initial amyloid-β accumulation occurs in Alzheimer's disease. This is the first study to show that individuals who have abnormal cerebrospinal amyloid-β42 but normal amyloid-β positron emission tomography have an increased cortical amyloid-β accumulation rate similar to those with both abnormal cerebrospinal fluid and positron emission tomography and higher rate than subjects where both modalities are normal. The results indicate that cerebrospinal fluid amyloid-β42 becomes abnormal in the earliest stages of Alzheimer's disease, before amyloid positron emission tomography and before neurodegeneration starts.", "New research criteria for preclinical Alzheimer's disease have been proposed, which include stages for cognitively normal individuals with abnormal amyloid markers (stage 1), abnormal amyloid and neuronal injury markers (stage 2), or abnormal amyloid and neuronal injury markers and subtle cognitive changes (stage 3). We aimed to investigate the prevalence and long-term outcome of preclinical Alzheimer's disease according to these criteria. Participants were cognitively normal (clinical dementia rating [CDR]=0) community-dwelling volunteers aged at least 65 years who were enrolled between 1998 and 2011 at the Washington University School of Medicine (MO, USA). CSF amyloid-β1-42 and tau concentrations and a memory composite score were used to classify participants as normal (both markers normal), preclinical Alzheimer's disease stage 1-3, or suspected non-Alzheimer pathophysiology (SNAP, abnormal injury marker without abnormal amyloid marker). The primary outcome was the proportion of participants in each preclinical AD stage. Secondary outcomes included progression to CDR at least 0·5, symptomatic Alzheimer's disease (score of at least 0·5 for memory and at least one other domain and cognitive impairments deemed to be due to Alzheimer's disease), and mortality. We undertook survival analyses using subdistribution and standard Cox hazards models and linear mixed models. Of 311 participants, 129 (41%) were classed as normal, 47 (15%) as stage 1, 36 (12%) as stage 2, 13 (4%) as stage 3, 72 (23%) as SNAP, and 14 (5%) remained unclassified. The 5-year progression rate to CDR at least 0·5, symptomatic Alzheimer's disease was 2% for participants classed as normal, 11% for stage 1, 26% for stage 2, 56% for stage 3, and 5% for SNAP. Compared with individuals classed as normal, participants with preclinical Alzheimer's disease had an increased risk of death after adjusting for covariates (hazard ratio 6·2, 95% CI 1·1-35·0; p=0·040). Preclinical Alzheimer's disease is common in cognitively normal elderly people and is associated with future cognitive decline and mortality. Thus, preclinical Alzheimer's disease could be an important target for therapeutic intervention. National Institute of Aging of the National Institutes of Health (P01-AG003991, P50-AG05681, P01-AG02676), Internationale Stichting Alzheimer Onderzoek, the Center for Translational Molecular Medicine project LeARN, the EU/EFPIA Innovative Medicines Initiative Joint Undertaking, and the Charles and Joanne Knight Alzheimer Research Initiative.", "BACE1 is the rate-limiting protease in the production of synaptotoxic β-amyloid (Aβ) species and hence one of the prime drug targets for potential therapy of Alzheimer's disease (AD). However, so far pharmacological BACE1 inhibition failed to rescue the cognitive decline in mild-to-moderate AD patients, which indicates that treatment at the symptomatic stage might be too late. In the current study, chronic in vivo two-photon microscopy was performed in a transgenic AD model to monitor the impact of pharmacological BACE1 inhibition on early β-amyloid pathology. The longitudinal approach allowed to assess the kinetics of individual plaques and associated presynaptic pathology, before and throughout treatment. BACE1 inhibition could not halt but slow down progressive β-amyloid deposition and associated synaptic pathology. Notably, the data revealed that the initial process of plaque formation, rather than the subsequent phase of gradual plaque growth, is most sensitive to BACE1 inhibition. This finding of particular susceptibility of plaque formation has profound implications to achieve optimal therapeutic efficacy for the prospective treatment of AD.", "To develop a novel cerebrospinal fluid (CSF) beta-secretase-1 activity assay and evaluate beta-secretase-1 (BACE-1) activity as a potential biomarker in human Alzheimer's disease. The assay consisted of an enzymatic reaction of CSF samples with an optimized beta-secretase peptide substrate and the cleavage products were detected using a neo-epitope specific antibody. The CSF BACE-1 activity assay described exhibits time, temperature, dose, and pH dependence, with sensitivity down to <1 pM of recombinant BACE-1 enzyme, and is completely blocked by BACE-1 inhibitors. The endogenous BACE-1 enzyme in CSF appears to exist as a c-terminally truncated protein, based on both western blotting and capture-based activity assays. In a small cohort of human subjects, an age-dependent increase in CSF BACE activity was observed (~1.0 pM/year, p<0.05). In Alzheimer's disease subjects, a significant decline in age-adjusted CSF BACE activity was observed compared to controls (56% in the log-transformed scale, p=0.02). We have developed a robust assay to measure CSF BACE-1 activity which could serve as a potential biomarker in human Alzheimer's disease subjects.", "We investigated the pattern of disease progression in the asymptomatic, mild cognitive impairment (MCI), and dementia stage of Alzheimer's disease (AD). We selected 284 subjects with AD pathology, defined as abnormal levels of amyloid beta 1-42 (Aβ1-42) in cerebrospinal fluid (CSF). Disease outcome measures included six biomarkers and five cognitive markers. We compared differences in baseline measures and decline over 4 years between the AD stages and tested whether these changes differed from subjects, without AD pathology (N = 132). CSF Aβ1-42 reached the maximum abnormality level in the asymptomatic stage and tau in the MCI stage. The imaging and cognitive markers started to decline in the asymptomatic stage, and decline accelerated with advancing clinical stage. This study provides further evidence for a temporal evolution of AD biomarkers. Our findings may be helpful to determine stage specific outcome measures for clinical trials.", "We conducted a meta-analysis of relationships between amyloid burden and cognition in cognitively normal, older adult humans. Methods of assessing amyloid burden included were CSF or plasma assays, histopathology, and PET ligands. Cognitive domains examined were episodic memory, executive function, working memory, processing speed, visuospatial function, semantic memory, and global cognition. Sixty-four studies representing 7,140 subjects met selection criteria, with 3,495 subjects from 34 studies representing independent cohorts. Weighted effect sizes were obtained for each study. Primary analyses were conducted limiting to independent cohort studies using only the most common assessment method (Pittsburgh compound B). Exploratory analyses included all assessment methods. Episodic memory (r = 0.12) had a significant relationship to amyloid burden. Executive function and global cognition did not have significant relationships to amyloid in the primary analysis of Pittsburgh compound B (r = 0.05 and r = 0.08, respectively), but did when including all assessment methods (r = 0.08 and r = 0.09, respectively). The domains of working memory, processing speed, visuospatial function, and semantic memory did not have significant relationships to amyloid. Differences in the method of amyloid assessment, study design (longitudinal vs cross-sectional), or inclusion of control variables (age, etc.) had little influence. Based on this meta-analytic survey of the literature, increased amyloid burden has small but nontrivial associations with specific domains of cognitive performance in individuals who are currently cognitively normal. These associations may be useful for identifying preclinical Alzheimer disease or developing clinical outcome measures." ]
The relationship between injected current to the soma and firing frequency	In the motor system, force gradation is achieved by recruitment of motoneurons and rate modulation of their firing frequency. Classical experiments investigating the relationship between injected current to the soma during intracellular recording and the firing frequency (the	[ "During voluntary muscle contraction, human motoneurones can exhibit specific discharge patterns: single and repetitive doublets. Delayed depolarization has been accepted as the mechanism underlying single doublets. Repetitive doublet firing has been studied much less and its controlling mechanisms remain obscure. The aim of the present study was to examine properties of repetitive doublets in human motoneurones and to consider their underlying potential mechanisms. It was found that 22 of 41 (53.7%) lower-threshold motor units (MUs) in the trapezius and 15 of 42 (35.7%) MUs in triceps brachii displayed repetitive doublets with the mean interspike intervals (ISIs) of 5.5 +/- 1.1 and 6.4 +/- 2.6 ms, respectively. Each doublet was followed by a prolonged post-doublet ISI. The analysis of properties of repetitive doublets showed that they were typically initiated in quiescent motoneurones rather than in firing ones (appearing just at recruitment in an all-or-none manner) and could only be maintained at a certain level of muscle contraction. Repetitive doublets were interrupted either voluntarily (by the subject), or spontaneously with sudden transition from doublet firing to single discharges-the firing behaviour that may be referred to as a firing-pattern \"jump\". The properties of doublet firing seem to be consistent with traits of motoneurone firing in the presence of plateau potentials reported in animal studies. It was suggested that the potential mechanisms underlying repetitive doublet firing could include a delayed depolarization as the primary determinant, which likely could become persistent probably due to a plateau potential activated in parallel with a common synaptic input.", "In the SOD1G93A mouse model of amyotrophic lateral sclerosis (ALS), a selective degeneration of fast-fatigable motor units and consequently an early decline of contractile force in individual fast-twitch muscles have been observed in the preclinical stage. However, most human muscles include fast and slow motor units. Gastrocnemius-soleus group (GS) contains such a mixture of units. We have investigated changes in the mechanical properties of GS at different SOD1G93A stages in mice. For this purpose, the tibial nerve was repetitively stimulated with rectangular pulses and the force of GS twitches was recorded using a strain gauge fixed to the Achilles tendon. Isometric and tetanic force were attenuated but not before the first clinical signs developed. However, already at preclinical stages, single twitches showed a slower decay compared to control. Consequently, fusion of GS twitches occurred at lower stimulus rates. Furthermore, already preclinically, the temporal course of successive twitch amplitudes changed during repetitive stimulation at increasing rates. The peak amplitudes as well as the potentiation following decay (fatigue) were lower in preclinical mice than in control. The time-lapse analysis of the contractile pattern as well as of the twitch configuration of the mixed muscle GS have revealed distinctive differences between wild-type controls and preclinical SOD1G93A mice. It would be of interest to know whether these preclinical changes are also detectable in ALS patients.", "The fast contraction time of mouse motor units creates a unique situation in which motoneurons have to fire at low frequencies to produce small forces but also at very high frequency (much higher than in cat or rat motoneurons) to reach the fusion frequency of their motor units. To understand how this problem is solved, we performed intracellular recordings of adult mouse spinal motoneurons and investigated systematically their subthreshold properties and their discharge pattern. We show that mouse motoneurons have a much wider range of firing frequencies than cat and rat motoneurons because of three salient features. First, they have a short membrane time constant. This results in a higher cutoff frequency and a higher resonance frequency, which allow mouse motoneurons to integrate inputs at higher frequencies. Second, their afterhyperpolarization (AHP) is faster, allowing the motoneurons to discharge at a higher rate. Third, motoneurons display high-frequency (100-150 Hz) subthreshold oscillations during the interspike intervals. The fast membrane kinetics greatly favors the appearance of these oscillations, creating a \"subprimary range\" of firing. In this range, which has never been reported in cat and in rat spinal motoneurons, the oscillations follow the AHP and trigger spiking after a variable delay, allowing a discharge at low frequency but at the expense of an irregular rate.", "1. In intracellular studies of cat lumbar motoneurones constant synaptic stimuli such as stretch, contraction or a high-frequency stimulation of a cut afferent nerve have been superimposed on firing in response to injected currents.2. As long as the slope relating spike frequency to injected current remained constant, which by definition is the ;primary range' of firing, algebraical summation of superimposed synaptic stimulation prevailed. Added quantities in these experiments were then between 2.0 and 56.2 impulses/sec for excitation, between -2.8 and -21.8 impulses/sec for inhibition.3. Data were obtained correlating firing rates with amount of synaptic potential and current respectively.4. Theoretical implications are dealt with in the Discussion.", "1. This paper extends the work on the ;primary range' of firing (Granit, Kernell & Lamarre, 1966), in lumbar motoneurones to the ;secondary range'. By definition the latter begins when, with stronger currents, the linear curve relating firing rate to injected current in the primary range undergoes a fairly sudden increase of slope.2. It was shown that motoneurones firing at the higher frequencies of the secondary range were partially inactivated. Yet such firing rates were within the physiological range.3. Algebraical summation of firing rates, when present in the secondary range, implied at the same time that the synaptic amount added was diminished by comparison with what it had been within the primary range.4. Superimposed synaptic excitatory stimuli did not (as in the ;primary range') regularly add their effect algebraically on to the rate of firing achieved by injected currents alone. More commonly the synaptic effect of the constant input underwent a progressive increase throughout the secondary range.5. Superimposed inhibitory stimuli regularly reduced the slope constant as determined by trans-membrane current alone and, by counter-acting inactivation, made the motoneurone approach the mode of firing characteristic of the ;primary range'.6. The latter finding emphasizes the significance of analysing firing motoneurones with the aid of ;slope constants' and provides inhibition with a new role in the integrative behaviour of motoneurones, as considered in the Discussion." ]
CYRI: an evolutionarily conserved regulator of actin-based protrusion	Actin-based protrusions are reinforced through positive feedback, but it is unclear what restricts their size, or limits positive signals when they retract or split. We identify an evolutionarily conserved regulator of actin-based protrusion: CYRI (CYFIP-related Rac interactor) also known as Fam49 (family of unknown function 49). CYRI binds activated Rac1 via a domain of unknown function (DUF1394) shared with CYFIP, defining DUF1394 as a Rac1-binding module. CYRI-depleted cells have broad lamellipodia enriched in Scar/WAVE, but reduced protrusion-retraction dynamics. Pseudopods induced by optogenetic Rac1 activation in CYRI-depleted cells are larger and longer lived. Conversely, CYRI overexpression suppresses recruitment of active Scar/WAVE to the cell edge, resulting in short-lived, unproductive protrusions. CYRI thus focuses protrusion signals and regulates pseudopod complexity by inhibiting Scar/WAVE-induced actin polymerization. It thus behaves like a 'local inhibitor' as predicted in widely accepted mathematical models, but not previously identified in cells. CYRI therefore regulates chemotaxis, cell migration and epithelial polarization by controlling the polarity and plasticity of protrusions.	[ "The Cdc42- and Rac-interactive binding motif (CRIB) of coronin binds to Rho GTPases with a preference for GDP-loaded Rac. Mutation of the Cdc42- and Rac-interactive binding motif abrogates Rac binding. This results in increased 1evels of activated Rac in coronin-deficient Dictyostelium cells (corA(-)), which impacts myosin II assembly. corA(-) cells show increased accumulation of myosin II in the cortex of growth-phase cells. Myosin II assembly is regulated by myosin heavy chain kinase-mediated phosphorylation of its tail. Kinase activity depends on the activation state of the p21-activated kinase a. The myosin II defect of corA(-) mutant is alleviated by dominant-negative p21-activated kinase a. It is rescued by wild-type coronin, whereas coronin carrying a mutated Cdc42- and Rac-interactive binding motif failed to rescue the myosin defect in corA(-) mutant cells. Ectopically expressed myosin heavy chain kinases affinity purified from corA(-) cells show reduced kinase activity. We propose that coronin through its affinity for GDP-Rac regulates the availability of GTP-Rac for activation of downstream effectors.", "Directional migration moves cells rapidly between points, whereas random migration allows cells to explore their local environments. We describe a Rac1 mechanism for determining whether cell patterns of migration are intrinsically random or directionally persistent. Rac activity promoted the formation of peripheral lamellae that mediated random migration. Decreasing Rac activity suppressed peripheral lamellae and switched the cell migration patterns of fibroblasts and epithelial cells from random to directionally persistent. In three-dimensional rather than traditional two-dimensional cell culture, cells had a lower level of Rac activity that was associated with rapid, directional migration. In contrast to the directed migration of chemotaxis, this intrinsic directional persistence of migration was not mediated by phosphatidylinositol 3'-kinase lipid signaling. Total Rac1 activity can therefore provide a regulatory switch between patterns of cell migration by a mechanism distinct from chemotaxis.", "Eukaryotic chemotaxis is extremely complex. Cells can sense a wide range of stimuli, and many intracellular pathways are simultaneously involved. Recent genetic analyses of the steps between receptors and cytoskeleton, and how the cell controls actin and pseudopod behaviour, have yielded exciting new data but still no coherent understanding of chemotaxis. However, concentrating on pseudopods themselves and the physical processes that regulate them, rather than the internal signalling pathways, can simplify the data and help resolve the underlying mechanism. Direct action of electric fields and physical forces on cell migration suggest that mechanical forces and force-generating proteins like actin and myosin are centrally important in steering cells during chemotaxis.", "Microtubule breakdown in the presence of 5 or 40 microg/ml of colchicine is observed in BHK-21/C13 fibroblast-like cells. Several morphological and physiological effects are noted in the absence of microtubules: (a) the cells transform from fibroblast-like to epithelial-like cells; (b) the normal pattern of intracellular birefringence changes and a juxtanuclear cap of birefringent filaments is formed; (c) time-lapse cinematography demonstrates that cell locomotion is inhibited in colchicine-treated cells, even though membrane ruffling persists. The results are discussed in terms of the specific roles of microtubules in cultured cell motility and possible functional relationships of the three types of cytoplasmic fibers seen in BHK-21 cells." ]
Inverting exosialidase: a new CAZy glycoside hydrolase family	Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.	[ "The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.", "We present a hierarchical genome-assembly process (HGAP) for high-quality de novo microbial genome assemblies using only a single, long-insert shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT) DNA sequencing. Our method uses the longest reads as seeds to recruit all other reads for construction of highly accurate preassembled reads through a directed acyclic graph-based consensus procedure, which we follow with assembly using off-the-shelf long-read assemblers. In contrast to hybrid approaches, HGAP does not require highly accurate raw reads for error correction. We demonstrate efficient genome assembly for several microorganisms using as few as three SMRT Cell zero-mode waveguide arrays of sequencing and for BACs using just one SMRT Cell. Long repeat regions can be successfully resolved with this workflow. We also describe a consensus algorithm that incorporates SMRT sequencing primary quality values to produce de novo genome sequence exceeding 99.999% accuracy.", "The determination of a large number of three-dimensional structures of glycosidases, both free and in complex with ligands, has provided valuable new insights into glycosidase catalysis, especially when coupled with results from studies of specifically labelled glycosidases and kinetic analyses of point mutants.", "Microorganisms are the most abundant and widely spread organisms on earth. They colonize a huge variety of natural and anthropogenic environments, including very specialized ecological niches and even extreme habitats, which are made possible by the immense metabolic diversity and genetic adaptability of microbes. As most of the organisms from environmental samples defy cultivation, cultivation-independent metagenomics approaches have been applied since more than one decade to access and characterize the phylogenetic diversity in microbial communities as well as their metabolic potential and ecological functions. Thereby, metagenomics has fully emerged as an own scientific field for mining new biocatalysts for many industrially relevant processes in biotechnology and pharmaceutics. This review summarizes common metagenomic approaches ranging from sampling, isolation of nucleic acids, construction of metagenomic libraries and their evaluation. Sequence-based screenings implement next-generation sequencing platforms, microarrays or PCR-based methods, while function-based analysis covers heterologous expression of metagenomic libraries in diverse screening setups. Major constraints and advantages of each strategy are described. The importance of alternative host-vector systems is discussed, and in order to underline the role of phylogenetic and physiological distance from the gene donor and the expression host employed, a case study is presented that describes the screening of a genomic library from an extreme thermophilic bacterium in both Escherichia coli and Thermus thermophilus. Metatranscriptomics, metaproteomics and single-cell-based methods are expected to complement metagenomic screening efforts to identify novel biocatalysts from environmental samples.", "Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution.", "Recent studies have shown that a number of glycoside hydrolase families do not follow the classical catalytic mechanisms, as they lack a typical catalytic base/nucleophile. A variety of mechanisms are used to replace this function, including substrate-assisted catalysis, a network of several residues, and the use of non-carboxylate residues or exogenous nucleophiles. Removal of the catalytic base/nucleophile by mutation can have a profound impact on substrate specificity, producing enzymes with completely new functions.", "Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32-bit desktop machine. Tablet is freely available for Microsoft Windows, Apple Mac OS X, Linux and Solaris. Fully bundled installers can be downloaded from http://bioinf.scri.ac.uk/tablet in 32- and 64-bit versions." ]
Antibacterial Activity of Chlorate	Nitrate respiration is a widespread mode of anaerobic energy generation used by many bacterial pathogens, and the respiratory nitrate reductase, Nar, has long been known to reduce chlorate to the toxic oxidizing agent chlorite. Here, we demonstrate the antibacterial activity of chlorate against	[ "The epidemiology of human brucellosis, the commonest zoonotic infection worldwide, has drastically changed over the past decade because of various sanitary, socioeconomic, and political reasons, together with the evolution of international travel. Several areas traditionally considered to be endemic--eg, France, Israel, and most of Latin America--have achieved control of the disease. On the other hand, new foci of human brucellosis have emerged, particularly in central Asia, while the situation in certain countries of the Near East (eg, Syria) is rapidly worsening. Furthermore, the disease is still present, in varying trends, both in European countries and in the USA. Awareness of this new global map of human brucellosis will allow for proper interventions from international public-health organisations.", "Ventilator-associated pneumonia is the most common infection in intensive care unit patients associated with high morbidity rates and elevated economic costs; Pseudomonas aeruginosa is one of the most frequent bacteria linked with this entity, with a high attributable mortality despite adequate treatment that is increased in the presence of multiresistant strains, a situation that is becoming more common in intensive care units. In this manuscript, we review the current management of ventilator-associated pneumonia due to P. aeruginosa, the most recent antipseudomonal agents, and new adjunctive therapies that are shifting the way we treat these infections. We support early initiation of broad-spectrum antipseudomonal antibiotics in present, followed by culture-guided monotherapy de-escalation when susceptibilities are available. Future management should be directed at blocking virulence; the role of alternative strategies such as new antibiotics, nebulized treatments, and vaccines is promising.", "A tool kit of vectors was designed to manipulate and express genes from a wide range of gram-negative species by using in vivo recombination. Saccharomyces cerevisiae can use its native recombination proteins to combine several amplicons in a single transformation step with high efficiency. We show that this technology is particularly useful for vector design. Shuttle, suicide, and expression vectors useful in a diverse group of bacteria are described and utilized. This report describes the use of these vectors to mutate clpX and clpP of the opportunistic pathogen Pseudomonas aeruginosa and to explore their roles in biofilm formation and surface motility. Complementation of the rhamnolipid biosynthetic gene rhlB is also described. Expression vectors are used for controlled expression of genes in two pseudomonad species. To demonstrate the facility of building complicated constructs with this technique, the recombination of four PCR-generated amplicons in a single step at >80% efficiency into one of these vectors is shown. These tools can be used for genetic studies of pseudomonads and many other gram-negative bacteria.", "Adaptation to oxygen deficiency is essential for virulence and persistence of Brucella inside the host. The flexibility of this bacterium with respect to oxygen depletion is remarkable, since Brucella suis can use an oxygen-dependent transcriptional regulator of the FnrN family, two high-oxygen-affinity terminal oxidases, and a complete denitrification pathway to resist various conditions of oxygen deficiency. Moreover, our previous results suggested that oxidative respiration and denitrification can be simultaneously used by B. suis under microaerobiosis. The requirement of a functional cytochrome bd ubiquinol oxidase for nitrite reductase expression evidenced the linkage of these two pathways, and the central role of the two-component system RegB/RegA in the coordinated control of both respiratory systems was demonstrated. We propose a scheme for global regulation of B. suis respiratory pathways by the transcriptional regulator RegA, which postulates a role for the cytochrome bd ubiquinol oxidase in redox signal transmission to the histidine sensor kinase RegB. More importantly, RegA was found to be essential for B. suis persistence in vivo within oxygen-limited target organs. It is conceivable that RegA acts as a controller of numerous systems involved in the establishment of the persistent state, characteristic of chronic infections by Brucella.", "Brucella strains encounter oxygen deprivation during their intracellular replication in host cells, and the capacity of these bacteria to utilize NO(3) as an alternative electron acceptor for respiration plays an important role in their successful adaption to their intracellular niche. In this issue of Molecular Microbiology, Carrica et al (2012). report that NtrY and NtrX comprise a redox-responsive two-component regulator in Brucella abortus 2308 that responds to decreasing levels of O(2) and induces the expression of this strain's denitrification genes. Thus, NtrYX joins the increasing number of genetic regulators that contribute to the metabolic versatility required for the virulence of Brucella strains in their mammalian hosts.", "Despite intensive eradication therapy, some CF patients with early Pseudomonas aeruginosa infection rapidly develop a chronic infection. To elucidate factors associated with this persistence, bacterial characteristics of early P. aeruginosa isolates were analysed that were either eradicated rapidly or persisted despite multiple antimicrobial treatments. Eighty-six early infection episodes were studied. First P. aeruginosa isolates from patients with eradication (36) or persistent infection (16) were included; isolates from patients with intermittent infection (34) were omitted from the study. Virulence assays, antimicrobial resistance, cytotoxicity and mutation frequencies were analysed in vitro. P. aeruginosa was genotyped by SNP-array. Transcriptomic profiles of two eradicated and two persistent strains were compared. Nineteen per cent of patients developed persistent infection; 42% achieved eradication. Secretion of virulence factors and mutation frequencies were highly variable among both eradicated and persistent isolates and were not different between the groups. Cytotoxicity was present in 57% of eradicated vs. 100% of persistent isolates (p <0.01). None of the isolates were resistant to antibiotics. The isolates were genotypically highly diverse. Multivariate analysis showed that in vitro determined bacterial characteristics could not predict persistence after first P. aeruginosa infection. Preliminary transcriptomic data showed increased expression of some genes related to a metabolic pathway. The early onset of chronic infection was not associated with (in vitro determined) bacterial characteristics only. Although the persistent isolates were more often cytotoxic, for the individual patient it was not possible to predict the risk of persistence based on bacterial characteristics. Unknown factors such as host-pathogen and pathogen-pathogen interactions should be further explored.", "Predicted highly expressed (PHX) genes in five currently available high G+C complete alpha-proteobacterial genomes are analyzed. These include: the nitrogen-fixing plant symbionts Sinorhizobium meliloti (SINME) and Mesorhizobium loti (MESLO), the nonpathogenic aquatic bacterium Caulobacter crescentus (CAUCR), the plant pathogen Agrobacterium tumefaciens (AGRTU), and the mammalian pathogen Brucella melitensis (BRUME). Three of these genomes, SINME, AGRTU, and BRUME, contain multiple chromosomes or megaplasmids (>1 Mb length). PHX genes in these genomes are concentrated mainly in the major (largest) chromosome with few PHX genes found in the secondary chromosomes and megaplasmids. Tricarboxylic acid cycle and aerobic respiration genes are strongly PHX in all five genomes, whereas anaerobic pathways of glycolysis and fermentation are mostly not PHX. Only in MESLO (but not SINME) and BRUME are most glycolysis genes PHX. Many flagellar genes are PHX in MESLO and CAUCR, but mostly are not PHX in SINME and AGRTU. The nonmotile BRUME also carries many flagellar genes but these are generally not PHX and all but one are located in the second chromosome. CAUCR stands out among available prokaryotic genomes with 25 PHX TonB-dependent receptors. These are putatively involved in uptake of iron ions and other nonsoluble compounds." ]
Excitation ratiometric kinase activity biosensors for real-time monitoring of neuronal plasticity	Unravelling the dynamic molecular interplay behind complex physiological processes such as neuronal plasticity requires the ability to both detect minute changes in biochemical states in response to physiological signals and track multiple signalling activities simultaneously. Fluorescent protein-based biosensors have enabled the real-time monitoring of dynamic signalling processes within the native context of living cells, yet most commonly used biosensors exhibit poor sensitivity (for example, due to low dynamic range) and are limited to imaging signalling activities in isolation. Here, we address this challenge by developing a suite of excitation ratiometric kinase activity biosensors that offer the highest reported dynamic range and enable the detection of subtle changes in signalling activity that could not be reliably detected previously, as well as a suite of single-fluorophore biosensors that enable the simultaneous tracking of as many as six distinct signalling activities in single living cells.	[ "In just three years, the green fluorescent protein (GFP) from the jellyfish Aequorea victoria has vaulted from obscurity to become one of the most widely studied and exploited proteins in biochemistry and cell biology. Its amazing ability to generate a highly visible, efficiently emitting internal fluorophore is both intrinsically fascinating and tremendously valuable. High-resolution crystal structures of GFP offer unprecedented opportunities to understand and manipulate the relation between protein structure and spectroscopic function. GFP has become well established as a marker of gene expression and protein targeting in intact cells and organisms. Mutagenesis and engineering of GFP into chimeric proteins are opening new vistas in physiological indicators, biosensors, and photochemical memories.", "The specificity of many signal transduction pathways relies on the temporal coordination of different second messenger signals. Here we found a molecular mechanism which guarantees that conventional protein kinase C (PKC) isoforms are sequentially activated by calcium and diacylglycerol signals. Receptor stimuli that triggered repetitive calcium spikes induced a parallel repetitive translocation of GFP-tagged PKCgamma to the plasma membrane. While calcium acted rapidly, diacylglycerol binding to PKCgamma was initially prevented by a pseudosubstrate clamp, which kept the diacylglycerol-binding site inaccessible and delayed calcium- and diacylglycerol-mediated kinase activation. After termination of calcium signals, bound diacylglycerol prolonged kinase activity. The properties of this molecular decoding machine make PKCgamma responsive to persistent diacylglycerol increases combined with high- but not low-frequency calcium spikes.", "Phospholipase C produces two second messengers--diacylglycerol (DAG), which remains in the membrane, and inositol triphosphate (IP(3)), which triggers the release of calcium ions (Ca(2+)) from intracellular stores. Genetically encoded sensors based on a single circularly permuted fluorescent protein (FP) are robust tools for studying intracellular Ca(2+) dynamics. We have developed a robust sensor for DAG based on a circularly permuted green FP that can be co-imaged with the red fluorescent Ca(2+) sensor R-GECO for simultaneous measurement of both second messengers." ]
Regulation of apoptosis-inducing factor in transmissible gastroenteritis virus-induced apoptosis	We previously demonstrated that transmissible gastroenteritis virus (TGEV) could induce apoptosis through caspase signaling. However, apoptosis was not completely prevented by caspases inhibitors, suggesting that there may be a caspase-independent pathway involved in TGEV-induced cell apoptosis. In this study, we investigated the regulation of apoptosis-inducing factor (AIF) on TGEV-induced apoptotic pathway. Results indicated that AIF translocated from the mitochondria to nucleus during TGEV infection, and the AIF inhibitor, N-phenylmaleimide (NP), significantly attenuated the apoptosis. In addition, the translocation of AIF was inhibited by Veliparib (ABT-888), an inhibitor of poly (ADP-ribose) polymerase (PARP). And the reactive oxygen species (ROS) scavenger, pyrrolidinedithiocarbamic (PDTC), redistributed AIF in the mitochondria and nucleus in TGEV-infected cells. Moreover, the protein levels in nucleus and the mRNA levels of AIF were inhibited in the presence of the p53 inhibitor, piﬁthrin-α (PFT-α) or in TGEV-infected p53-/-cells. Furthermore, TGEV-induced apoptosis was blocked by combination of three or more inhibitors, such as pan caspase inhibitor Z-VAD-FMK, NP, ABT-888, PDTC, PFT-α, to treat PK-15 cells. Taken together, these results suggest that the p53- and ROS-mediated AIF pathway and caspase-dependent pathway were involved in TGEV-induced apoptosis.	[ "The tumor suppressor protein p53 is a redox-active transcription factor that organizes and directs cellular responses in the face of a variety of stresses that lead to genomic instability. One of the most important questions in the study of p53 is how selective transactivation of certain p53 target genes is achieved. Reactive oxygen species (ROS), generated by cells as products or by-products, can function either as signaling molecules or as cellular toxicants. Cellular generation of ROS is central to redox signaling. Recent studies have revealed that each cellular concentration and distribution of p53 has a distinct cellular function and that ROS act as both an upstream signal that triggers p53 activation and a downstream factor that mediates apoptosis. Here, we examine the newly discovered role of p53 in regulating cellular ROS generation and how ROS modulate selective transactivation of p53 target genes. The focus is on interlinks between ROS and p53.", "Transmissible gastroenteritis virus (TGEV) infection induced apoptosis in several cell lines in vitro. Our previous studies demonstrated that TGEV could activate FasL- and mitochondria-mediated pathways to induce apoptosis in PK-15 cells. In this study, we investigated the regulation of p53 and p38 mitogen-activated protein kinases (MAPK) signalling pathways in the interaction of TGEV with host cells. We observed that TGEV infection decreased p300/CBP, downregulated MDM2 and promoted p53 phosphorylation at serines 15, 20 and 46, resulting in accumulation and activation of p53 in PK-15 cells. TGEV infection induced the transient activation of p38 MAPK in the early phase of inoculation and constant activation in the later phase of infection. However, UV-irradiated TGEV did not promote the activation of p53 and p38 MAPK in the later phase, whereas it only triggered the transient activation of p38 MAPK in the early phase. Blocking of p53 activation significantly inhibited the occurrence of apoptosis through suppressing the TGEV-induced FasL expression, Bcl-2 reduction, Bax and cytochrome c redistribution, while inhibition of p38 activity moderately blocked apoptosis induction and partly attenuated the accumulation and activation of p53. However, inhibition of p38 and p53 activity had no significant effects on viral gene transcription at 12 and 24 h post-infection. Taken together, these results demonstrated that TGEV infection promoted the activation of p38 MAPK and p53 signalling, and p53 signalling might play a dominant role in the regulation of cell apoptosis. These findings provide new insights into the function of p53 and p38 MAPK in the interaction of TGEV with host cells.", "Porcine circovirus type 2 (PCV2) is a ubiquitous pathogen in the swine industry worldwide. Previous studies have shown that PCV2 infection induces host cell apoptosis through up-regulation of p53. To further identify the regulatory roles of p53 signaling in the process of PCV2 infection, we established p53 gene knockout PK15 cell lines using the genomic editor tool CRISPR/Cas9, and further investigated the roles of p53 in modulating the cell cycle and viral replication in this study. The results show that PCV2 infection induced obvious S phase accumulation in wild-type PK15 cells and a compromised S phase accumulation in the p53 gene mutation cells (813PK15 p53m/m ), but did not induce obvious S phase accumulation in the p53 gene knockout cells (148PK15 p53-/-) compared with the respective mock infection. PCV2 infection activated p53 signaling, up-regulated the expression of p21, Cyclin E, and down-regulated Cyclin A, CDK2. In p53 deficient cells, however, PCV2-induced changes in Cyclin A, CDK2, and Cyclin E were efficiently reversed to the basal levels. Detection of PCV2 replication showed decreased viral ORF1 genomic DNA in p53 deficient cells (148PK15 p533-/-) and p53 mutated cells (813PK15 p53m/m ) compared with p53 wild-type cells after different synchronization treatment. Furthermore, PCV2 viral genomic DNA and Cap protein levels were higher in the cells released from S phase synchronized cells than in the cells released from the G0/G1 phase or G2/M phase-synchronized, or asynchronous cells after 18 h post-infection. Taken together, this study demonstrates that PCV2 infection induces S phase accumulation to favor viral replication in host cells through activation of the p53 pathway.", "An appropriate control over cell cycle progression depends on many factors. Cyclin-dependent kinase (CDK) inhibitor p21 (also known as p21(WAF1/Cip1)) is one of these factors that promote cell cycle arrest in response to a variety of stimuli. The inhibitory effect of P21 on cell cycle progression correlates with its nuclear localization. P21 can be induced by both p53-dependent and p53-independent mechanisms. Some other important functions attributed to p21 include transcriptional regulation, modulation or inhibition of apoptosis. These functions are largely dependent on direct p21/protein interactions and also on p21 subcellular localizations. In addition, p21 can play a role in DNA repair by interacting with proliferating cell nuclear antigen (PCNA). In this review, we will focus on the multiple functions of p21 in cell cycle regulation, apoptosis and gene transcription after DNA damage and briefly discuss the pathways and factors that have critical roles in p21 expression and activity.", "The present study assesses the oxidative burst activity from polymorphonuclear leukocytes (PMNLs) from bovine leukemia virus (BLV)-infected cows. Fifteen clinically healthy cows were divided into serologically positive cows without any hematological alteration, serologically positive animals with persistent lymphocytosis (PL) and healthy serologically negative cows. The oxidative burst activity from the PMNLs was evaluated by flow cytometry using 2',7'-dichlorofluorescein diacetate as a probe. PMNLs from each cow were incubated with heat-killed Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) to stimulate oxidative burst activity. The results of the present work showed no significant difference in the oxidative burst activity without any stimulus and elicited by S. aureus. Conversely, a decrease in the oxidative burst index induced by E. coli in PMNLs was observed in BLV-infected cows.", "Inhibition of homologous recombination (HR) is believed to be a transactivation-independent function of p53 that protects from genetic instability. Misrepair by HR can lead to genetic alterations such as translocations, duplications, insertions and loss of heterozygosity, which all bear the risk of driving oncogenic transformation. Regulation of HR by wild-type p53 (wtp53) should prevent these genomic rearrangements. Mutation of p53 is a frequent event during carcinogenesis. In particular, dominant-negative mutants inhibiting wtp53 expressed from the unperturbed allel can drive oncogenic transformation by disrupting the p53-dependent anticancer barrier. Here, we asked whether the hot spot mutants R175H and R273H relax HR control in p53-proficient cells. Utilizing an I-SceI-based reporter assay, we observed a moderate (1.5 × ) stimulation of HR upon expression of the mutant proteins in p53-proficient CV-1, but not in p53-deficient H1299 cells. Importantly, the stimulatory effect was exactly paralleled by an increase in the number of HR competent S- and G2-phase cells, which can well explain the enhanced recombination frequencies. Furthermore, the impact on HR exerted by the transactivation domain double-mutant L22Q/W23S and mutant R273P, both of which were reported to regulate HR independently of G1-arrest execution, is also exactly mirrored by cell-cycle behavior. These results are in contrast to previous concepts stating that the transactivation-independent impact of p53 on HR is a general phenomenon valid for replication-associated and also for directly induced double-strand break. Our data strongly suggest that the latter is largely mediated by cell-cycle regulation, a classical transactivation-dependent function of p53." ]
Recalling Cigarette Advertisements in Convenience Stores	This study examined the extent to which visitors to convenience stores remember the cigarette advertisements they encounter in these stores and investigated the relationships between how advertisements are recalled and attitudes toward them.	[ "Tobacco use is the most important preventable risk factor for premature death. The World Health Organization (WHO) Framework Convention on Tobacco Control (FCTC), the first international public health treaty, came into force in 2005. This paper reviews the present status of tobacco control policies in Korea according to the WHO FCTC recommendations. In Korea, cigarette use is high among adult males (48.2% in 2010), and cigarette prices are the lowest among the Organization for Economic Cooperation and Development countries with no tax increases since 2004. Smoke-free policies have shown incremental progress since 1995, but smoking is still permitted in many indoor public places. More than 30% of non-smoking adults and adolescents are exposed to second-hand smoke. Public education on the harmful effects of tobacco is currently insufficient and the current policies have not been adequately evaluated. There is no comprehensive ban on tobacco advertising, promotion, or sponsorship in Korea. Cigarette packages have text health warnings on only 30% of the main packaging area, and misleading terms such as \"mild\" and \"light\" are permitted. There are nationwide smoking cessation clinics and a Quitline service, but cessation services are not covered by public insurance schemes and there are no national treatment guidelines. The sale of tobacco to minors is prohibited by law, but is poorly enforced. The socioeconomic inequality of smoking prevalence has widened, although the government considers inequality reduction to be a national goal. The tobacco control policies in Korea have faltered recently and priority should be given to the development of comprehensive tobacco control policies.", "The tobacco retail environment is a crucial marketing medium for the industry. A 2009 review found evidence of a positive association between exposure to point-of-sale (POS) tobacco promotion and increased smoking and smoking susceptibility, though limitations in the evidence base were identified. We reviewed and critically appraised recent evidence documenting the influence of POS tobacco promotion, and POS tobacco display bans, on smoking-related behavior and cognitions. We reviewed original quantitative and qualitative research that examined the relationship between POS tobacco promotion and smoking prevalence, individual-level smoking and quitting and tobacco purchasing behavior, smoking susceptibility, and smoking-related cognitions. Twenty peer-reviewed studies (18 quantitative and 2 qualitative) met the inclusion criteria; each study reported findings consistent with a positive association between exposure to POS tobacco promotion and smoking or smoking susceptibility. Several studies met key criteria for causality: 4 indicated a dose-response association, 2 prospective studies were identified, and evidence from intervention studies supported the reversibility of the association. Findings were consistent across different study designs, settings, and measures. The existing evidence supports a positive association between exposure to POS tobacco promotion and smoking. This review provides evidence to support the continuation of POS tobacco display bans in those jurisdictions where such legislation has been introduced and strengthens the evidence encouraging similar policies in jurisdictions without a POS display ban.", "To assess the impact of the Western Australian tobacco point-of-sale display ban on spontaneous purchase behaviours. Daily adult smokers (n=402) observed purchasing cigarettes were recruited via exit interviews either 2 months before or after the implementation of the display ban. Smokers were asked if they had intended to purchase cigarettes before entering the store to assess spontaneous purchase behaviours. Whether smokers had noticed the displays before their purchase and the extent to which this influenced their purchase decision was also assessed via non-prompting questions. When compared with before the ban, fewer smokers after the ban noticed the displays (27.1% vs 1.1%, p<0.001), fewer reported making spontaneous purchases (28.2% vs 19.8%, p<0.05) and fewer claimed the displays influenced their purchase decisions (free recall 5.0% vs 1.1%, p<0.05; cued recall 22.1% vs 3.8%, p<0.001). Before the ban, spontaneous purchasers were more likely than planned purchasers to suggest the displays influenced their purchase decisions (free recall 9.7% vs 3.2%, p<0.05; cued recall 40.0% vs 17.9%, p<0.01). After the ban, spontaneous purchasers nominating the influence of displays fell substantially (free recall 9.7% vs 5.6%, p=NS; cued recall 40.0% vs 11.1%, p<0.01) as it did for planned purchasers (free recall 3.2% vs 0.0%, p<0.05; cued recall 17.9% vs 2.1%, p<0.01). We observed a 30% reduction in smokers making spontaneous tobacco purchases after implementation of the Western Australian tobacco display ban and between a fivefold and sixfold reduction in the proportion suggesting displays influenced their decision to purchase cigarettes. These data are consistent with previous research suggesting tobacco displays encourage spontaneous purchases and their removal corresponds to reductions in the same.", "The aim of this study was to examine trends of socioeconomic differentials in smoking rates by gender, age, and socioeconomic position in South Korea. We used data from five Social Statistical Surveys of Korea National Statistical Office from 1989 to 2003. This study included 344,969 men and women aged 20 or over. Socioeconomic position indicators were education and occupation. Age-standardized smoking rates decreased in all age groups of men and women aged 45+ between 1989 and 2003, while smoking rates among women aged 20-44 did not decrease. Education was inversely associated with smoking in both genders. Those with manual occupations had greater smoking rates than those who performed non-manual labor. Based on the relative index of inequality, unfavorable inequality trends toward low education were detected in both genders aged 20-44. However, these trends were not found at ages 45-64. For occupational class, the relative inequality in smoking measured by odds ratios remained stable among men and women between 1995 and 2003. Continuous and progressive anti-smoking policy measures should be directed toward South Korean men whose smoking rates are still high. Policy efforts to reduce socioeconomic inequality in smoking, especially among young adult men and women, should be exercised. In addition, additional anti-smoking policy measures toward young women's smoking habits need to be developed in South Korea." ]
Mycobiota in host physiology and disease	Mammalian barrier surfaces are densely populated by symbiont fungi in much the same way the former are colonized by symbiont bacteria. The fungal microbiota, otherwise known as the mycobiota, is increasingly recognized as a critical player in the maintenance of health and homeostasis of the host. Here we discuss the impact of the mycobiota on host physiology and disease, the factors influencing mycobiota composition, and the current technologies used for identifying symbiont fungal species. Understanding the tripartite interactions among the host, mycobiota, and other members of the microbiota, will help to guide the development of novel prevention and therapeutic strategies for a variety of human diseases. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Organismal Models.	[ "Manipulation of the gut microbiota holds great promise for the treatment of inflammatory and allergic diseases. Although numerous probiotic microorganisms have been identified, there remains a compelling need to discover organisms that elicit more robust therapeutic responses, are compatible with the host, and can affect a specific arm of the host immune system in a well-controlled, physiological manner. Here we use a rational approach to isolate CD4(+)FOXP3(+) regulatory T (Treg)-cell-inducing bacterial strains from the human indigenous microbiota. Starting with a healthy human faecal sample, a sequence of selection steps was applied to obtain mice colonized with human microbiota enriched in Treg-cell-inducing species. From these mice, we isolated and selected 17 strains of bacteria on the basis of their high potency in enhancing Treg cell abundance and inducing important anti-inflammatory molecules--including interleukin-10 (IL-) and inducible T-cell co-stimulator (ICOS)--in Treg cells upon inoculation into germ-free mice. Genome sequencing revealed that the 17 strains fall within clusters IV, XIVa and XVIII of Clostridia, which lack prominent toxins and virulence factors. The 17 strains act as a community to provide bacterial antigens and a TGF-β-rich environment to help expansion and differentiation of Treg cells. Oral administration of the combination of 17 strains to adult mice attenuated disease in models of colitis and allergic diarrhoea. Use of the isolated strains may allow for tailored therapeutic manipulation of human immune disorders.", "Human skin, the body's largest organ, functions as a physical barrier to bar the entry of foreign pathogens, while concomitantly providing a home to myriad commensals. Over a human's life span, keratinized skin cells, immune cells, and microbes all interact to integrate the processes of maintaining skin's physical and immune barrier under homeostatic healthy conditions and also under multiple stresses, such as wounding or infection. In this Review, we explore the intricate interactions of microbes and immune cells on the skin surface and within associated appendages to regulate this orchestrated maturation in the context of both host physiological changes and environmental challenges.", "The human gut contains trillions of microorganisms that influence our health by metabolizing xenobiotics, including host-targeted drugs and antibiotics. Recent efforts have characterized the diversity of this host-associated community, but it remains unclear which microorganisms are active and what perturbations influence this activity. Here, we combine flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the gut contains a distinctive set of active microorganisms, primarily Firmicutes. Short-term exposure to a panel of xenobiotics significantly affected the physiology, structure, and gene expression of this active gut microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding antibiotic resistance, drug metabolism, and stress response pathways. These results demonstrate the power of moving beyond surveys of microbial diversity to better understand metabolic activity, highlight the unintended consequences of xenobiotics, and suggest that attempts at personalized medicine should consider interindividual variations in the active human gut microbiome.", "The intestinal microflora, typically equated with bacteria, influences diseases such as obesity and inflammatory bowel disease. Here, we show that the mammalian gut contains a rich fungal community that interacts with the immune system through the innate immune receptor Dectin-1. Mice lacking Dectin-1 exhibited increased susceptibility to chemically induced colitis, which was the result of altered responses to indigenous fungi. In humans, we identified a polymorphism in the gene for Dectin-1 (CLEC7A) that is strongly linked to a severe form of ulcerative colitis. Together, our findings reveal a eukaryotic fungal community in the gut (the \"mycobiome\") that coexists with bacteria and substantially expands the repertoire of organisms interacting with the intestinal immune system to influence health and disease.", "Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.", "The microbial communities that inhabit the intestinal tract are essential for mammalian health. Communication between the microbiota and the host establishes and maintains immune homeostasis, enabling protective immune responses against pathogens while preventing adverse inflammatory responses to harmless commensal microbes. Specific bacteria, such as segmented filamentous bacteria, Clostridium species, and Bacteroides fragilis, are key contributors to immune homeostasis in the gut. The cellular and molecular interactions between intestinal microbes and the immune system are rapidly being elucidated. Here, we review advances in our understanding of the microbial populations that shape the mucosal immune system and create a protective defense that prevents infection while tolerating friendly commensals.", "The composite human microbiome of Western populations has probably changed over the past century, brought on by new environmental triggers that often have a negative impact on human health. Here we show that consumption of a diet high in saturated (milk-derived) fat, but not polyunsaturated (safflower oil) fat, changes the conditions for microbial assemblage and promotes the expansion of a low-abundance, sulphite-reducing pathobiont, Bilophila wadsworthia. This was associated with a pro-inflammatory T helper type 1 (T(H)1) immune response and increased incidence of colitis in genetically susceptible Il10(−/−), but not wild-type mice. These effects are mediated by milk-derived-fat-promoted taurine conjugation of hepatic bile acids, which increases the availability of organic sulphur used by sulphite-reducing microorganisms like B. wadsworthia. When mice were fed a low-fat diet supplemented with taurocholic acid, but not with glycocholic acid, for example, a bloom of B. wadsworthia and development of colitis were observed in Il10(−/−) mice. Together these data show that dietary fats, by promoting changes in host bile acid composition, can markedly alter conditions for gut microbial assemblage, resulting in dysbiosis that can perturb immune homeostasis. The data provide a plausible mechanistic basis by which Western-type diets high in certain saturated fats might increase the prevalence of complex immune-mediated diseases like inflammatory bowel disease in genetically susceptible hosts." ]
Pseudomonads as natural control agents in the phyllosphere of winter wheat	Natural control of phytopathogenic microorganisms is assumed as a priority function of the commensal plant microbiota. In this study, the suitability of fluorescent pseudomonads in the phyllosphere of crop plants as natural control agents was evaluated. Under field conditions, ears of winter wheat were found to be colonized with high consistency and at a high density by pseudomonads at the late milk dough stage. Isolates of these bacteria were evaluated for their potential to protect the plants from phytopathogenic	[ "Fusarium graminearum causes Fusarium head blight (FHB), a devastating disease that leads to extensive yield and quality loss of wheat and barley. Bacteria isolated from wheat kernels and plant anthers were screened for antagonistic activity against F. graminearum. Based on its in vitro effectiveness, strain SG6 was selected for characterization and identified as Bacillus subtilis. B. subtilis SG6 exhibited a high antifungal effect on the mycelium growth, sporulation and DON production of F. graminearum with the inhibition rate of 87.9%, 95.6% and 100%, respectively. In order to gain insight into biological control effect in situ, we applied B. subtilis SG6 at anthesis through the soft dough stage of kernel development in field test. It was revealed that B. subtilis SG6 significantly reduced disease incidence (DI), FHB index and DON (P ≤ 0.05). Further, ultrastructural examination shows that B. subtilis SG6 strain induced stripping of F. graminearum hyphal surface by destroying the cellular structure. When hypha cell wall was damaged, the organelles and cytoplasm inside cell would exude, leading to cell death. The antifungal activity of SG6 could be associated with the coproduction of chitinase, fengycins and surfactins.", "Efforts to reduce mycotoxin contamination in food logically start with minimizing plant infection by mycotoxin producing pathogens. Fusarium graminearum (perfect state, Gibberella zeae) infects wheat heads at flowering, causing the disease Fusarium head blight (FHB) and losses of over 2.6 billion dollars in the U.S. during the last 10 years. The pathogen often produces deoxynivalenol (DON) resulting in grain size and quality reduction. Highly resistant wheat cultivars currently are not available for reducing FHB, and labeled fungicides are not consistently effective. The feasibility of biologically controlling FHB is currently being evaluated. Microbial isolates obtained from wheat anthers were screened for their ability to utilize tartaric acid, a compound that is poorly utilized by F. graminearum and could be utilized in formulations of biological control agents. Four strains that utilized tartaric acid and three that did not were effective in reducing FHB disease severity by up to 95% in greenhouse and 56% in field trials. Additional research programs around the globe have identified other antagonist strains with potential for biologically controlling FHB. Though a considerable body of research remains to be completed, strategies and microorganisms for biologically controlling FHB have reached an advanced stage of development and offer the promise of being an effective tool that could soon contribute to the reduction of FHB severity and DON contamination of grain in commercial agriculture.", "Some soil bacteria protect plants against soil-borne diseases by producing toxic secondary metabolites. Such beneficial biocontrol bacteria can be used in agricultural systems as alternative to agrochemicals. The broad spectrum toxins responsible for plant protection also inhibit predation by protozoa and nematodes, the main consumers of bacteria in soil. Therefore, predation pressure may favour biocontrol bacteria and contribute to plant health. We analyzed the effect of Acanthamoeba castellanii on semi-natural soil bacterial communities in a microcosm experiment. We determined the frequency of culturable bacteria carrying genes responsible for the production of the antifungal compounds 2,4-diacetylphloroglucinol (DAPG), pyrrolnitrin (PRN) and hydrogen cyanide (HCN) in presence and absence of A. castellanii. We then measured if amoebae affected soil suppressiveness in a bioassay with sugar beet seedlings confronted to the fungal pathogen Rhizoctonia solani. Amoebae increased the frequency of both DAPG and HCN positive bacteria in later plant growth phases (2 and 3 weeks), as well as the average number of biocontrol genes per bacterium. The abundance of DAPG positive bacteria correlated with disease suppression, suggesting that their promotion by amoebae may enhance soil health. However, the net effect of amoebae on soil suppressiveness was neutral to slightly negative, possibly because amoebae slow down the establishment of biocontrol bacteria on the recently emerged seedlings used in the assay. The results indicate that microfaunal predators foster biocontrol bacterial communities. Understanding interactions between biocontrol bacteria and their predators may thus help developing environmentally friendly management practices of agricultural systems.", "The present study was conducted to evaluate the potential of rice rhizosphere associated antagonistic bacteria for growth promotion and disease suppression of bacterial leaf blight (BLB). A total of 811 rhizospheric bacteria were isolated and screened against 3 prevalent strains of BLB pathogen Xanthomonas oryzae pv. oryzae (Xoo) of which five antagonistic bacteria, i.e., Pseudomonas spp. E227, E233, Rh323, Serratia sp. Rh269 and Bacillus sp. Rh219 showed antagonistic potential (zone of inhibition 1-19 mm). Production of siderophores was found to be the common biocontrol determinant and all the strains solubilized inorganic phosphate (82-116 μg mL-1) and produced indole acetic acid (0.48-1.85 mg L-1) in vitro. All antagonistic bacteria were non-pathogenic to rice, and their co-inoculation significantly improved plant health in terms of reduced diseased leaf area (80%), improved shoot length (31%), root length (41%) and plant dry weight (60%) as compared to infected control plants. Furthermore, under pathogen pressure, bacterial inoculation resulted in increased activity of defense related enzymes including phenylalanine ammonia-lyase and polyphenol oxidase, along with 86% increase in peroxidase and 53% increase in catalase enzyme activities in plants inoculated with Pseudomonas sp. Rh323 as well as co-inoculated plants. Bacterial strains showed good colonization potential in the rice rhizosphere up to 21 days after seed inoculation. Application of bacterial consortia in the field resulted in an increase of 31% in grain yield and 10% in straw yield over non-inoculated plots. Although, yield increase was statistically non-significant but was accomplished with overall saving of 20% chemical fertilizers. The study showed that Pseudomonas sp. Rh323 can be used to develop dual-purpose inoculum which can serve not only to suppress BLB but also to promote plant growth in rice.", "Plants host distinct bacterial communities on and inside various plant organs, of which those associated with roots and the leaf surface are best characterized. The phylogenetic composition of these communities is defined by relatively few bacterial phyla, including Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype-dependent fine-tuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate leaf surface. Both the leaf and root microbiota contain bacteria that provide indirect pathogen protection, but root microbiota members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant microbiota emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth-promoting and plant health-promoting bacteria." ]
Evolutionary Novelties in the Avian Syrinx	In its most basic conception, a novelty is simply something new. However, when many previously proposed evolutionary novelties have been illuminated by genetic, developmental, and fossil data, they have refined and narrowed our concept of biological "newness." For example, they show that these novelties can occur at one or multiple levels of biological organization. Here, we review the identity of structures in the avian vocal organ, the syrinx, and bring together developmental data on airway patterning, structural data from across tetrapods, and mathematical modeling to assess what is novel. In contrast with laryngeal cartilages that support vocal folds in other vertebrates, we find no evidence that individual cartilage rings anchoring vocal folds in the syrinx have homology with any specific elements in outgroups. Further, unlike all other vertebrate vocal organs, the syrinx is not derived from a known valve precursor, and its origin involves a transition from an evolutionary "spandrel" in the respiratory tract, the site where the trachea meets the bronchi, to a target for novel selective regimes. We find that the syrinx falls into an unusual category of novel structures: those having significant functional overlap with the structures they replace. The syrinx, along with other evolutionary novelties in sensory and signaling modalities, may more commonly involve structural changes that contribute to or modify an existing function rather than those that enable new functions.	[ "The mouse has been the dominant model organism in studies on the development, genetics and evolution of the mammalian skull and associated soft-tissue for decades. There is the potential to take advantage of this well studied model and the range of mutant, knockin and knockout organisms with diverse craniofacial phenotypes to investigate the functional significance of variation and the role of mechanical forces on the development of the integrated craniofacial skeleton and musculature by using computational mechanical modelling methods (e.g. finite element and multibody dynamic modelling). Currently, there are no detailed published data of the mouse masticatory musculature available. Here, using a combination of micro-dissection and non-invasive segmentation of iodine-enhanced micro-computed tomography, we document the anatomy, architecture and proportions of the mouse masticatory muscles. We report on the superficial masseter (muscle, tendon and pars reflecta), deep masseter, zygomaticomandibularis (anterior, posterior, infraorbital and tendinous parts), temporalis (lateral and medial parts), external and internal pterygoid muscles. Additionally, we report a lateral expansion of the attachment of the temporalis onto the zygomatic arch, which may play a role in stabilising this bone during downwards loading. The data presented in this paper now provide a detailed reference for phenotypic comparison in mouse models and allow the mouse to be used as a model organism in biomechanical and functional modelling and simulation studies of the craniofacial skeleton and particularly the masticatory system.", "Sexual selection is proposed to be an important driver of diversification in animal systems, yet previous tests of this hypothesis have produced mixed results and the mechanisms involved remain unclear. Here, we use a novel phylogenetic approach to assess the influence of sexual selection on patterns of evolutionary change during 84 recent speciation events across 23 passerine bird families. We show that elevated levels of sexual selection are associated with more rapid phenotypic divergence between related lineages, and that this effect is restricted to male plumage traits proposed to function in mate choice and species recognition. Conversely, we found no evidence that sexual selection promoted divergence in female plumage traits, or in male traits related to foraging and locomotion. These results provide strong evidence that female choice and male-male competition are dominant mechanisms driving divergence during speciation in birds, potentially linking sexual selection to the accelerated evolution of pre-mating reproductive isolation.", "High resolution X-ray computed tomography (CT), or microCT, is a promising and already widely used technique in various scientific fields. Also for histological purposes it has great potential. Although microCT has proven to be a valuable technique for the imaging of bone structures, the visualization of soft tissue structures is still an important challenge due to their low inherent X-ray contrast. One way to achieve contrast enhancement is to make use of contrast agents. However, contrary to light and electron microscopy, knowledge about contrast agents and staining procedures is limited for X-ray CT. The purpose of this paper is to identify useful X-ray contrast agents for soft tissue visualization, which can be applied in a simple way and are also suited for samples larger than (1 cm)(3) . And 28 chemical substances have been investigated. All chemicals were applied in the form of concentrated aqueous solutions in which the samples were immersed. First, strips of green Bacon were stained to evaluate contrast enhancement between muscle and adipose tissue. Furthermore it was also tested whether the contrast agents remained fixed in the tissue after staining by re-immersing them in water. Based on the results, 12 contrast agents were selected for further testing on postmortem mice hind legs, containing a variety of different tissues, including muscle, fat, bone, cartilage and tendons. It was evaluated whether the contrast agents allowed a clearer distinction between the different soft tissue structures present. Finally also penetration depth was measured. And 26 chemicals resulted in contrast enhancement between muscle and adipose tissue in the Bacon strips. Mercury(II)chloride (HgCl2 ), phosphotungstic acid (PTA), phosphomolybdic acid (PMA) and ammonium orthomolybdate ((NH4 )2 MoO4 ) remained fixed after re-immersion in water. The penetration tests showed that potassium iodide (KI) and sodium tungstate can be most efficiently used for large samples of the order of several tens of cm(3) . PMA, PTA, HgCl2 and also to a lesser extent Na2 WO4 and (NH4 )2 MoO4 allowed a clearer distinction between the different soft tissue structures present.", "Baleen whales (Mysticeti) are the largest animals on Earth, thanks to their ability to filter huge volumes of small prey from seawater. Mysticetes appeared during the Late Eocene, but evidence of their early evolution remains both sparse and controversial [1, 2], with several models competing to explain the origin of baleen-based bulk feeding [3-6]. Here, we describe a virtually complete skull of Llanocetus denticrenatus, the second-oldest (ca. 34 Ma) mysticete known. The new material represents the same individual as the type and only specimen, a fragmentary mandible. Phylogenetic analysis groups Llanocetus with the oldest mysticete, Mystacodon selenensis [2], into the basal family Llanocetidae. Llanocetus is gigantic (body length ∼8 m) compared to other early mysticetes [7-9]. The broad rostrum has sharp, widely spaced teeth with marked dental abrasion and attrition, suggesting biting and occlusal shearing. As in extant mysticetes, the palate bears many sulci, commonly interpreted as osteological correlates of baleen [3]. Unexpectedly, these sulci converge on the upper alveoli, suggesting a peri-dental blood supply to well-developed gums, rather than to inter-alveolar racks of baleen. We interpret Llanocetus as a raptorial or suction feeder, revealing that whales evolved gigantism well before the emergence of filter feeding. Rather than driving the origin of mysticetes, baleen and filtering most likely only arose after an initial phase of suction-assisted raptorial feeding [2, 4, 5]. This scenario differs strikingly from that proposed for odontocetes, whose defining adaptation-echolocation-was present even in their earliest representatives [10].", "The site and physiologic mechanism(s) responsible for the generation of odontocete biosonar signals have eluded investigators for decades. To address these issues we subjected postmortem toothed whale heads to interrogation using medical imaging techniques. Most of the 40 specimens (from 19 species) were examined using x-ray computed tomography (CT) and/or magnetic resonance imaging (MR). Interpretation of scan images was aided by subsequent dissection of the specimens or, in one case, by cryosectioning. In all specimens we described a similar tissue complex and identified it as the hypothetical biosonar signal generator. This complex includes a small pair of fatty bursae embedded in a pair of connective tissue lips, a cartilaginous blade, a stout ligament, and an array of soft tissue air sacs. Comparing and contrasting the morphologic patterns of nasal structures across species representing every extant odontocete superfamily reveals probable homologous relationships, which suggests that all toothed whales may be making their biosonar signals by a similar mechanism.", "The structural variation of the gekkonid larynx and trachea is examined within a representative subset of 17 species of Afro-Madagascan gekkonines to determine if there are underlying morphological correlates of vocalization. The documented morphology is compared to that of the tokay (Gekko gecko), which has previously been described. Data were obtained from gross anatomical observations, scanning electron microscopy, histological examinations and computer-generated, three-dimensional, skeletal reconstructions. Although there is limited variation among most Afro-Malagasy gekkonids, the larynges of Ptenopus garrulus and Uroplatus fimbriatus exhibit marked degrees of differentiation, suggesting that laryngeal and tracheal morphology may account for the documented vocal variability of gekkonid lizards. Cladistic analyses indicated that parallel adaptive trends characterize the laryngeal morphology of the examined taxa. Alternate designs and refinements to a model of gekkonid phonation are presented, and the evolution of acoustic communication in the Gekkonidae is considered.", "The International Mouse Phenotyping Consortium (IMPC) plans to phenotype 20,000 single-gene knockout mice to gain an insight into gene function. Approximately 30% of these knockout mouse lines will be embryonic or perinatal lethal. The IMPC has selected three-dimensional (3D) imaging to phenotype these mouse lines at relevant stages of embryonic development in an attempt to discover the cause of lethality using detailed anatomical information. Rate of throughput is paramount as IMPC production centers have been given the ambitious task of completing this phenotyping project by 2021. Sifting through the wealth of data within high-resolution 3D mouse embryo data sets by trained human experts is infeasible at this scale. Here, we present a phenotyping pipeline that identifies statistically significant anatomical differences in the knockout, in comparison with the wild type, through a computer-automated image registration algorithm. This phenotyping pipeline consists of three analyses (intensity, deformation, and atlas based) that can detect missing anatomical structures and differences in volume of whole organs as well as on the voxel level. This phenotyping pipeline was applied to micro-CT images of two perinatal lethal mouse lines: a hypomorphic mutation of the Tcf21 gene (Tcf21-hypo) and a knockout of the Satb2 gene. With the proposed pipeline we were able to identify the majority of morphological phenotypes previously published for both the Tcf21-hypo and Satb2 mutant mouse embryos in addition to novel phenotypes. This phenotyping pipeline is an unbiased, automated method that highlights only those structural abnormalities that survive statistical scrutiny and illustrates them in a straightforward fashion." ]
Genome-wide association studies and expression quantitative trait loci analysis to identify genetic variants associated with residual feed intake in Irish beef cattle	Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10	[ "KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).", "The recent success of genome-wide association studies (GWAS) is now followed by the challenge to determine how the reported susceptibility variants mediate complex traits and diseases. Expression quantitative trait loci (eQTLs) have been implicated in disease associations through overlaps between eQTLs and GWAS signals. However, the abundance of eQTLs and the strong correlation structure (LD) in the genome make it likely that some of these overlaps are coincidental and not driven by the same functional variants. In the present study, we propose an empirical methodology, which we call Regulatory Trait Concordance (RTC) that accounts for local LD structure and integrates eQTLs and GWAS results in order to reveal the subset of association signals that are due to cis eQTLs. We simulate genomic regions of various LD patterns with both a single or two causal variants and show that our score outperforms SNP correlation metrics, be they statistical (r(2)) or historical (D'). Following the observation of a significant abundance of regulatory signals among currently published GWAS loci, we apply our method with the goal to prioritize relevant genes for each of the respective complex traits. We detect several potential disease-causing regulatory effects, with a strong enrichment for immunity-related conditions, consistent with the nature of the cell line tested (LCLs). Furthermore, we present an extension of the method in trans, where interrogating the whole genome for downstream effects of the disease variant can be informative regarding its unknown primary biological effect. We conclude that integrating cellular phenotype associations with organismal complex traits will facilitate the biological interpretation of the genetic effects on these traits.", "The last few years have seen the development of large efforts for the analysis of genome function, especially in the context of genome variation. One of the most prominent directions has been the extensive set of studies on expression quantitative trait loci (eQTLs), namely, the discovery of genetic variants that explain variation in gene expression levels. Such studies have offered promise not just for the characterization of functional sequence variation but also for the understanding of basic processes of gene regulation and interpretation of genome-wide association studies. In this review, we discuss some of the key directions of eQTL research and its implications.", "MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying variation in this measure of feed efficiency in bovines.", "Numerous genome-wide screens for polymorphisms that influence gene expression have provided key insights into the genetic control of transcription. Despite this work, the relevance of specific polymorphisms to in vivo expression and splicing remains unclear. We carried out the first genome-wide screen, to our knowledge, for SNPs that associate with alternative splicing and gene expression in human primary cells, evaluating 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. We identified 23 high confidence associations with total expression and 80 with alternative splicing as reflected by expression levels of specific exons. Fewer than 50% of the implicated SNPs however show effects in both tissue types, reflecting strong evidence for distinct genetic control of splicing and expression in the two tissue types. The data generated here also suggest the possibility that splicing effects may be responsible for up to 13 out of 84 reported genome-wide significant associations with human traits. These results emphasize the importance of establishing a database of polymorphisms affecting splicing and expression in primary tissue types and suggest that splicing effects may be of more phenotypic significance than overall gene expression changes.", "Mechanisms underlying variation in residual feed intake (RFI), a heritable feed efficiency measure, are poorly understood while the relationship between RFI and meat quality is uncertain. To address these issues, 2 divergent cohorts consisting of High (HRFI) and Low (LRFI) RFI individuals were created by assessing RFI in 48 Angus-sired steers during a 70 d feeding trial to identify steers with divergent RFI. The association of RFI with indices of meat quality and expression of genes within hypothalamic and adipose tissue was then determined in LRFI and HRFI steers. While on test, feed intake was recorded daily with BW and hip heights recorded at 14 d intervals. Ultrasound measurements of rib eye area (REA) and backfat (BF) were recorded initially and before harvest. Carcass and growth data were analyzed using a mixed model with RFI level (LRFI, HRFI) as the independent variable. The least-square means (lsmeans) for RFI were -1.25 and 1.51 for the LRFI and HRFI cohorts (P < .0001). Dry matter intake was higher for the HRFI individuals versus the LRFI steers (P < .0001) while on test BW gain was not different between the 2 groups (P < 0.73). There were no differences detected in marbling score (P < 0.93), BF (P < 0.61), REA (P < 0.15), yield grade (P < 0.85) or objective Hunter color measures between LRFI and HRFI steers indicating that there was no relationship between RFI and meat quality. Neuropeptide-Y (NPY), relaxin-3 (RLN3), melanocortin 4 receptor (MC4R), and GnRH mRNA expression was 64%, 59%, 58%, 86% lower (P < 0.05), respectively, while gonadotropin inhibiting hormone (GnIH) and pro-opiomelanocortin (POMC) mRNA expression was 198% and 350% higher (P < 0.01) in the arcuate nucleus of LRFI steers. Expression of agouti-related protein (AGRP), relaxin/insulin-like family peptide receptor 1 (RXFP1), and melanocortin 3 receptor mRNA was similar between LRFI and HRFI animals. Pituitary expression of FSHβ (P < 0.03) and LHβ (P < 0.01) was correlated to hypothalamic GnRH levels suggesting that changes in gene expression within the arcuate nucleus had functional consequences. Leptin mRNA expression was 245% higher in the adipose tissue of LRFI steers consistent with lower levels of NPY and higher expression of POMC in their hypothalami. These data support the hypothesis that differences in hypothalamic neuropeptide gene expression underlie variation in feed efficiency in steers while the gonadotropin axis may also influence feed efficiency.", "We have previously reported the altered expressions of HSPF1 and LIM in the lymphoblastoid cell lines (LCLs) derived from Japanese patients with bipolar disorder (bipolar I disorder). The altered expression at the LCL level would be useful for developing diagnostic markers as well as a cellular model for bipolar disorder. In this study, we extended our previous study by measuring their expressions using the following samples: (1) larger number of LCLs from Japanese subjects, (2) LCLs from Caucasian subjects, and (3) LCLs from patients with bipolar II disorder or schizophrenia. We confirmed the increased expression of HSPF1 (P=0.009) and decreased expression of LIM (P=0.001) in the LCLs from patients with Japanese bipolar I disorder. These altered expressions were also observed in those from patients with Japanese bipolar II disorder (P= 0.002 for HSPF1 and P = 0.072 for LIM). We also found the altered expressions of HSPF1 in LCLs from Caucasian patients with bipolar II disorder (P=0.011) and LIM in those from patients with schizophrenia (P = 0.001)." ]
is hmga2 a risk gene?	The high mobility group AT hook 2 (HMGA2) gene was previously identified in a genome-wide association study as a candidate risk gene that might be related to polycystic ovary syndrome (PCOS). Whether HMGA2 contributes to promoting granulosa cell (GC) proliferation in PCOS remains unknown.	[ "Although variants in the IGF2BP2/IMP2 gene confer risk for type 2 diabetes, IMP2, an RNA binding protein, is not known to regulate metabolism. Imp2(-/-) mice gain less lean mass after weaning and have increased lifespan. Imp2(-/-) mice are highly resistant to diet-induced obesity and fatty liver and display superior glucose tolerance and insulin sensitivity, increased energy expenditure, and better defense of core temperature on cold exposure. Imp2(-/-) brown fat and Imp2(-/-) brown adipocytes differentiated in vitro contain more UCP1 polypeptide than Imp2(+/+) despite similar levels of Ucp1 mRNA; the Imp2(-/-)adipocytes also exhibit greater uncoupled oxygen consumption. IMP2 binds the mRNAs encoding Ucp1 and other mitochondrial components, and most exhibit increased translational efficiency in the absence of IMP2. In vitro IMP2 inhibits translation of mRNAs bearing the Ucp1 untranslated segments. Thus IMP2 limits longevity and regulates nutrient and energy metabolism in the mouse by controlling the translation of its client mRNAs.", "To further understanding of the genetic basis of type 2 diabetes (T2D) susceptibility, we aggregated published meta-analyses of genome-wide association studies (GWAS), including 26,488 cases and 83,964 controls of European, east Asian, south Asian and Mexican and Mexican American ancestry. We observed a significant excess in the directional consistency of T2D risk alleles across ancestry groups, even at SNPs demonstrating only weak evidence of association. By following up the strongest signals of association from the trans-ethnic meta-analysis in an additional 21,491 cases and 55,647 controls of European ancestry, we identified seven new T2D susceptibility loci. Furthermore, we observed considerable improvements in the fine-mapping resolution of common variant association signals at several T2D susceptibility loci. These observations highlight the benefits of trans-ethnic GWAS for the discovery and characterization of complex trait loci and emphasize an exciting opportunity to extend insight into the genetic architecture and pathogenesis of human diseases across populations of diverse ancestry.", "Are there any correlations between the phenotypes of polycystic ovary syndrome (PCOS) and the genotypes of the PCOS susceptibility single nucleotide polymorphisms (SNPs) in THADA, DENND1A and LHCGR? The PCOS susceptibility genes, THADA and DENND1A, carry risk alleles that are associated with endocrine and metabolic disturbances in patients with PCOS. PCOS is a heterogeneous endocrinopathy characterized by oligo-anovulation, hyperandrogenism and polycystic ovaries. In a previous genome-wide association study, the SNP variants rs13429458, rs12478601, rs2479106, rs10818854 and rs13405728 in the THADA, DENND1A and LHCGR genes were identified as being independently associated with PCOS. The aim of this study was to identify any additional correlations between the phenotypes of PCOS and genotypes of the five SNPs described in the previous study. In the present cross-sectional study, a total of 1731 PCOS patients and 4964 controls were enrolled. Patients were diagnosed according to Rotterdam criteria. Clinical information was collected from the patients and controls. Endocrine and metabolic parameters were evaluated for phenotype-genotype correlation analyses. Using a recessive model, the AA group for rs13429458 in THADA was associated with increased luteinizing hormone (LH) (P < 0.01) and testosterone (T) (P = 0.02) levels in subjects with PCOS; the LH/follicle-stimulating hormone ratio was also higher in the AA group (P < 0.01). Also using a recessive model, the CC genotype of rs12478601, also in THADA, was associated with increased levels of low-density lipoprotein (P = 0.02). Using a dominant model, the GG + AG group for rs2479106 in DENND1A was associated with elevated serum insulin levels 2 h after a glucose load in the patients with PCOS (P = 0.02). All of the comparisons were adjusted for age and BMI. The relatively younger age of the participants may represent a considerable bias when evaluating metabolic alterations as a function of different genotypes, as significant metabolic disturbances may emerge later in life. Furthermore, the sample sizes of several sub-genotype groups were relatively small; to some extent this limited the statistical power of the analysis. The PCOS susceptibility genes, THADA and DENND1A, carry risk alleles that are associated with endocrine and metabolic disturbances in PCOS patients of Han Chinese descent. The findings have shown genuine heterogeneity, stratified on the basis of both clinical findings and genotypes. Replication of these results is expected in other ethnic groups.", "Women with polycystic ovary syndrome (PCOS) are insulin resistant, have insulin secretory defects, and are at high risk for glucose intolerance. We performed this study to determine the prevalence of glucose intolerance and parameters associated with risk for this in PCOS women. Two-hundred and fifty-four PCOS women, aged 14-44 yr, were prospectively evaluated at 2 centers, 1 urban and ethnically diverse (n = 110) and 1 rural and ethnically homogeneous (n = 144). The rural PCOS women were compared to 80 control women of similar weight, ethnicity, and age. A 75-g oral glucose challenge was administered after a 3-day 300-g carbohydrate diet and an overnight fast with 0 and 2 h blood samples for glucose levels. Diabetes was categorized according to WHO criteria. The prevalence of glucose intolerance was 31.1% impaired glucose intolerance (IGT) and 7.5% diabetes. In nonobese PCOS women (body mass index, <27 kg/m2), 10.3% IGT and 1.5% diabetes were found. The prevalence of glucose intolerance was significantly higher in PCOS vs. control women (chi2 = 7.0; P = 0.01; odds ratio = 2.76; 95% confidence interval = 1.23-6.57). Variables most associated with postchallenge glucose levels were fasting glucose levels (P < 0.0001), PCOS status (P = 0.002), waist/hip ratio (P = 0.01), and body mass index (P = 0.021). The American Diabetes Association criteria applied to fasting glucose significantly underdiagnosed diabetes compared to the WHO criteria (3.2% vs. 7.5%; chi2 = 4.7; P = 0.046; odds ratio = 2.48; 95% confidence interval = 1.01-6.69). We conclude that 1) PCOS women are at significantly increased risk for IGT and type 2 diabetes mellitus at all weights and at a young age; 2) these prevalence rates are similar in 2 different populations of PCOS women, suggesting that PCOS may be a more important risk factor than ethnicity or race for glucose intolerance in young women; and 3) the American Diabetes Association diabetes diagnostic criteria failed to detect a significant number of PCOS women with diabetes by postchallenge glucose values." ]
Factors associated with self-care practice among adult diabetes patients in public hospitals of West Shoa Zone, Oromia Regional State, Ethiopia	Diabetes, a rising global health problem, requires continuous self-care practice to prevent acute and chronic complications. However, studies show that few diabetes patients practice the recommended self-care in Ethiopia. The aim of this study was to assess factors associated with self-care practice among adult diabetes patients in public hospitals of West Shoa Zone, Oromia Regional State, Ethiopia.	[ "To examine the effectiveness of the health system response to the challenge of diabetes across different settings and explore the inequalities in diabetes care that are attributable to socioeconomic factors. We used nationally representative health examination surveys from Colombia, England, the Islamic Republic of Iran, Mexico, Scotland, Thailand and the United States of America to obtain data on diagnosis, treatment and control of hyperglycaemia, arterial hypertension and hypercholesterolaemia among individuals with diabetes. Using logistic regression, we explored the socioeconomic determinants of diagnosis and effective case management. A substantial proportion of individuals with diabetes remain undiagnosed and untreated, both in developed and developing countries. The figures range from 24% of the women in Scotland and the USA to 62% of the men in Thailand. The proportion of individuals with diabetes reaching treatment targets for blood glucose, arterial blood pressure and serum cholesterol was very low, ranging from 1% of male patients in Mexico to about 12% in the United States. Income and education were not found to be significantly related to the rates of diagnosis and treatment anywhere except in Thailand, but in the three countries with available data insurance status was a strong predictor of diagnosis and effective management, especially in the United States. There are many missed opportunities to reduce the burden of diabetes through improved control of blood glucose levels and improved diagnosis and treatment of arterial hypertension and hypercholesterolaemia. While no large socioeconomic inequalities were noted in the management of individuals with diabetes, financial access to care was a strong predictor of diagnosis and management.", "To describe the extent of problem of diabetes in rural India based on review of available literature and examine the secular trends over a period of 15 years i.e. from 1994 to 2009. A systematic search was performed using electronic as well as manual methods. Studies providing details of sample size, age group of participants, criteria used for diagnosis, along with the prevalence of any of the three outcomes of interest i.e. diabetes mellitus, impaired fasting glucose (IFG) or impaired glucose tolerance (IGT), were included. Analysis of secular trends reveals an increase in diabetes prevalence among rural population at a rate of 2.02 per 1000 population per year. The rate of increase was high in males (3.33 per 1000 per year) as compared to females (0.88 per 1000 per year). High prevalence of IFG and IGT has been observed in southern and northern parts of the country. The prevalence of diabetes is rising in rural India. There is a large pool of subjects with IFG and IGT at high risk of conversion to overt diabetes. Population-level and individual-level measures are needed to combat this increasing burden of diabetes.", "One of the global targets for non-communicable diseases is to halt, by 2025, the rise in the age-standardised adult prevalence of diabetes at its 2010 levels. We aimed to estimate worldwide trends in diabetes, how likely it is for countries to achieve the global target, and how changes in prevalence, together with population growth and ageing, are affecting the number of adults with diabetes. We pooled data from population-based studies that had collected data on diabetes through measurement of its biomarkers. We used a Bayesian hierarchical model to estimate trends in diabetes prevalence-defined as fasting plasma glucose of 7.0 mmol/L or higher, or history of diagnosis with diabetes, or use of insulin or oral hypoglycaemic drugs-in 200 countries and territories in 21 regions, by sex and from 1980 to 2014. We also calculated the posterior probability of meeting the global diabetes target if post-2000 trends continue. We used data from 751 studies including 4,372,000 adults from 146 of the 200 countries we make estimates for. Global age-standardised diabetes prevalence increased from 4.3% (95% credible interval 2.4-7.0) in 1980 to 9.0% (7.2-11.1) in 2014 in men, and from 5.0% (2.9-7.9) to 7.9% (6.4-9.7) in women. The number of adults with diabetes in the world increased from 108 million in 1980 to 422 million in 2014 (28.5% due to the rise in prevalence, 39.7% due to population growth and ageing, and 31.8% due to interaction of these two factors). Age-standardised adult diabetes prevalence in 2014 was lowest in northwestern Europe, and highest in Polynesia and Micronesia, at nearly 25%, followed by Melanesia and the Middle East and north Africa. Between 1980 and 2014 there was little change in age-standardised diabetes prevalence in adult women in continental western Europe, although crude prevalence rose because of ageing of the population. By contrast, age-standardised adult prevalence rose by 15 percentage points in men and women in Polynesia and Micronesia. In 2014, American Samoa had the highest national prevalence of diabetes (>30% in both sexes), with age-standardised adult prevalence also higher than 25% in some other islands in Polynesia and Micronesia. If post-2000 trends continue, the probability of meeting the global target of halting the rise in the prevalence of diabetes by 2025 at the 2010 level worldwide is lower than 1% for men and is 1% for women. Only nine countries for men and 29 countries for women, mostly in western Europe, have a 50% or higher probability of meeting the global target. Since 1980, age-standardised diabetes prevalence in adults has increased, or at best remained unchanged, in every country. Together with population growth and ageing, this rise has led to a near quadrupling of the number of adults with diabetes worldwide. The burden of diabetes, both in terms of prevalence and number of adults affected, has increased faster in low-income and middle-income countries than in high-income countries. Wellcome Trust.", "The prevalence of diabetes is rapidly increasing worldwide. Type 2 diabetes may remain undetected for many years, leading to severe complications and healthcare costs. This paper provides estimates of the prevalence of undiagnosed diabetes mellitus (UDM), using available data from high quality representative population-based sources. Data sources reporting both diagnosed and previously undiagnosed diabetes were identified and selected according to previously described IDF methodology for diabetes in adults (aged 20-79). Countries were divided into 15 data regions based on their geographic IDF Region and World Bank income classification. The median UDM proportion was calculated from selected data sources for each of data region. The number of UDM cases in 2013 was calculated from country, age and sex-specific estimates of known diabetes cases and data region-specific UDM proportion. Of 744 reviewed data sources, 88 sources representing 74 countries had sufficient information and were selected for generation of estimates of UDM. Globally, 45.8%, or 174.8 million of all diabetes cases in adults are estimated to be undiagnosed, ranging from 24.1% to 75.1% across data regions. An estimated 83.8% of all cases of UDM are in low- and middle-income countries. At a country level, Pacific Island nations have the highest prevalence of UDM. There is a high proportion of UDM globally, and especially in developing countries. Further high-quality studies of UDM are needed to strengthen future estimates.", "There is concern about an emerging diabetes epidemic in Turkey. We aimed to determine the prevalence of diagnosed and undiagnosed diabetes, prediabetes and their 12-year trends and to identify risk factors for diabetes in the adult Turkish population. A cross-sectional, population-based survey, 'TURDEP-II' included 26,499 randomly sampled adults aged ≥ 20 years (response rate: 87 %). Fasting glucose and biochemical parameters were measured in all; then a OGTT was performed to identify diabetes and prediabetes in eligible participants. The prevalence of diabetes was 16.5 % (new 7.5 %), translating to 6.5 million adults with diabetes in Turkey. It was higher in women than men (p = 0.008). The age-standardized prevalence to the TURDEP-I population (performed in 1997-98) was 13.7 % (if same diagnostic definition was applied diabetes prevalence is calculated 11.4 %). The prevalence of isolated-IFG and impaired glucose tolerance (IGT), and combined prediabetes was 14.7, 7.9, and 8.2 %, respectively; and that of obesity 36 % and hypertension 31.4 %. Compared to TURDEP-I; the rate of increase for diabetes: 90 %, IGT: 106 %, obesity: 40 % and central obesity: 35 %, but hypertension decreased by 11 % during the last 12 years. In women age, waist, body mass index (BMI), hypertension, low education, and living environment; in men age, BMI, and hypertension were independently associated with an increased prevalence of diabetes. In women current smoking, and in men being single were associated with a reduced risk. These results from one of the largest nationally representative surveys carried out so far show that diabetes has rapidly become a major public health challenge in Turkey. The figures are alarming and underscore the urgent need for national programs to prevent diabetes, to manage the illness and thus prevent complications.", "The Africa Region (AFR), where diabetes was once rare, has witnessed a surge in the condition. Estimates for type 1 diabetes suggest that about 39,000 people suffer from the disease in 2013 with 6.4 new cases occurring per year per 100,000 people in children <14 years old. Type 2 diabetes prevalence among 20-79-year-olds is 4.9% with the majority of people with diabetes <60 years old; the highest proportion (43.2%) is in those aged 40-59 years. Figures are projected to increase with the numbers rising from 19.8 million in 2013 to 41.5 million in 2035, representing a 110% absolute increase. There is an apparent increase in diabetes prevalence with economic development in AFR with rates of 4.4% in low-income, 5.0% in lower-middle income and 7.0% in upper-middle income countries. In addition to development and increases in life-expectancy, the likely progression of people at high risk for the development of type 2 diabetes will drive the expected rise of the disease. This includes those with impaired glucose tolerance, the prevalence of which is 7.3% among 20-79-year-olds in 2013. Mortality attributable to diabetes in 2013 in AFR is expected to be over half a million with three-quarter of these deaths occurring in those <60 years old. The prevalence of undiagnosed diabetes remains unacceptably high at 50.7% and is much higher in low income (75.1%) compared to lower- and upper-middle income AFR countries (46.0%). This highlights the inadequate response of local health systems which need to provide accessible, affordable and optimal care for diabetes.", "Diabetes is a major lifestyle disorder, the prevalence of which is increasing globally. Asian countries contribute to more than 60% of the world's diabetic population as the prevalence of diabetes is increasing in these countries. Socio-economic growth and industrialization are rapidly occurring in many of these countries. The urban-rural divide in prevalence is narrowing as urbanization is spreading widely, adversely affecting the lifestyle of populations. Asians have a strong ethnic and genetic predisposition for diabetes and have lower thresholds for the environmental risk factors. As a result, they develop diabetes at a younger age and at a lower body mass index and waist circumference when compared with the Western population. The adverse effect of physical inactivity and fatty food are manifested as the increasing rate of overweightness and obesity, even among children. The health care budgets for the disease management are meager and the health care outcome is far from the optimum. As a result, complications of diabetes are common and the economic burden is very high, especially among the poor strata of the society. National endeavors are urgently needed for early diagnosis, effective management and for primary prevention of diabetes. This editorial aims to highlight the rising trend in prevalence of diabetes in Asia, its causative factors and the urgent need to implement national strategies for primary prevention of type 2 diabetes." ]
Replay in the human hippocampus prioritizes weakly learned information and predicts subsequent memory performance	The hippocampus replays experiences during quiet rest periods, and this replay benefits subsequent memory. A critical open question is how memories are prioritized for this replay. We used functional magnetic resonance imaging (fMRI) pattern analysis to track item-level replay in the hippocampus during an awake rest period after participants studied 15 objects and completed a memory test. Objects that were remembered less well were replayed more during the subsequent rest period, suggesting a prioritization process in which weaker memories-memories most vulnerable to forgetting-are selected for replay. In a second session 12 hours later, more replay of an object during a rest period predicted better subsequent memory for that object. Replay predicted memory improvement across sessions only for participants who slept during that interval. Our results provide evidence that replay in the human hippocampus prioritizes weakly learned information, predicts subsequent memory performance, and relates to memory improvement across a delay with sleep.	[ "Practicing a motor skill triggers a process of memory consolidation that continues for hours after practice has ended, and becomes manifest in an improved skill at later testing. We used a sequential motor task (finger-to-thumb opposition task) to show that, in humans, the formation of motor skill memories essentially benefits from sleep. Independent of whether placed during daytime or nighttime, sleep after practice enhanced speed of sequence performance on average by 33.5% and reduced error rate by 30.1% as compared with corresponding intervals of wakefulness. The effect of sleep after learning proved to be stable when retesting was postponed for another night, to exclude effects of sleep loss and to assure that all subjects had sufficient sleep before retrieval testing. Also, the consolidating effect of sleep was specific for the motor sequence learned. It did not generalize to a similar sequence containing identical movement segments in a different order. Retention periods of wakefulness improved performance only moderately and only if placed during daytime. The observations demonstrate a critical role of sleep for storing and optimizing motor skills.", "The hippocampus is critical for spatial learning and memory. Hippocampal neurons in awake animals exhibit place field activity that encodes current location, as well as sharp-wave ripple (SWR) activity during which representations based on past experiences are often replayed. The relationship between these patterns of activity and the memory functions of the hippocampus is poorly understood. We interrupted awake SWRs in animals learning a spatial alternation task. We observed a specific learning and performance deficit that persisted throughout training. This deficit was associated with awake SWR activity, as SWR interruption left place field activity and post-experience SWR reactivation intact. These results provide a link between awake SWRs and hippocampal memory processes, which suggests that awake replay of memory-related information during SWRs supports learning and memory-guided decision-making.", "Sleep facilitates memory consolidation. A widely held model assumes that this is because newly encoded memories undergo covert reactivation during sleep. We cued new memories in humans during sleep by presenting an odor that had been presented as context during prior learning, and so showed that reactivation indeed causes memory consolidation during sleep. Re-exposure to the odor during slow-wave sleep (SWS) improved the retention of hippocampus-dependent declarative memories but not of hippocampus-independent procedural memories. Odor re-exposure was ineffective during rapid eye movement sleep or wakefulness or when the odor had been omitted during prior learning. Concurring with these findings, functional magnetic resonance imaging revealed significant hippocampal activation in response to odor re-exposure during SWS.", "The hippocampus is required for the encoding, consolidation and retrieval of event memories. Although the neural mechanisms that underlie these processes are only partially understood, a series of recent papers point to awake memory replay as a potential contributor to both consolidation and retrieval. Replay is the sequential reactivation of hippocampal place cells that represent previously experienced behavioral trajectories and occurs frequently in the awake state, particularly during periods of relative immobility. Awake replay may reflect trajectories through either the current environment or previously visited environments that are spatially remote. The repetition of learned sequences on a compressed time scale is well suited to promote memory consolidation in distributed circuits beyond the hippocampus, suggesting that consolidation occurs in both the awake and sleeping animal. Moreover, sensory information can influence the content of awake replay, suggesting a role for awake replay in memory retrieval.", "Learning is assumed to induce specific changes in neuronal activity during sleep that serve the consolidation of newly acquired memories. To specify such changes, we measured electroencephalographic (EEG) coherence during performance on a declarative learning task (word pair associations) and subsequent sleep. Compared with a nonlearning control condition, learning performance was accompanied with a strong increase in coherence in several EEG frequency bands. During subsequent non-rapid eye movement sleep, coherence only marginally increased in a global analysis of EEG recordings. However, a striking and robust increase in learning-dependent coherence was found when analyses were performed time-locked to the occurrence of slow oscillations (<1 Hz). Specifically, the surface-positive half-waves of the slow oscillation resulting from widespread cortical depolarization were associated with distinctly enhanced coherence after learning in the slow-oscillatory, delta, slow-spindle, and gamma bands. The findings identify the depolarizing phase of the slow oscillations in humans as a time period particularly relevant for a reprocessing of memories in sleep.", "The brain encodes huge amounts of information, but only a small fraction is stored for a longer time. There is now compelling evidence that the long-term storage of memories preferentially occurs during sleep. However, the factors mediating the selectivity of sleep-associated memory consolidation are poorly understood. Here, we show that the mere expectancy that a memory will be used in a future test determines whether or not sleep significantly benefits consolidation of this memory. Human subjects learned declarative memories (word paired associates) before retention periods of sleep or wakefulness. Postlearning sleep compared with wakefulness produced a strong improvement at delayed retrieval only if the subjects had been informed about the retrieval test after the learning period. If they had not been informed, retrieval after retention sleep did not differ from that after the wake retention interval. Retention during the wake intervals was not affected by retrieval expectancy. Retrieval expectancy also enhanced sleep-associated consolidation of visuospatial (two-dimensional object location task) and procedural motor memories (finger sequence tapping). Subjects expecting the retrieval displayed a robust increase in slow oscillation activity and sleep spindle count during postlearning slow-wave sleep (SWS). Sleep-associated consolidation of declarative memory was strongly correlated to slow oscillation activity and spindle count, but only if the subjects expected the retrieval test. In conclusion, our work shows that sleep preferentially benefits consolidation of memories that are relevant for future behavior, presumably through a SWS-dependent reprocessing of these memories.", "Sleep slow-wave activity (SWA) is thought to reflect sleep need, increasing in proportion to the previous time awake and decreasing during sleep, although the underlying mechanisms are unclear. Recent studies have shown that procedures presumably leading to local plastic changes in the cerebral cortex can lead to local changes in SWA during subsequent sleep. To further investigate the connection between cortical plasticity and sleep SWA, in this study we used a paired associative stimulation (PAS) protocol, in which median nerve stimuli were followed at different intervals (25 or 10 ms) by transcranial magnetic stimulation (TMS) pulses to the contralateral cortical hand area. As expected, such a protocol led to a sustained increase (long-term potentiation-like) or decrease (long-term depression-like) of cortical excitability as measured by motor evoked potentials. By using a TMS-compatible high-density electroencephalographic (EEG) system, we also found that, in individual subjects, TMS-evoked cortical responses over sensorimotor cortex changed with different interstimulus intervals. Moreover, during subsequent sleep, SWA increased locally in subjects whose TMS-evoked cortical responses had increased after PAS, and decreased in subjects whose cortical responses had decreased. Changes in TMS-evoked cortical EEG response and change in sleep SWA were localized to similar cortical regions and were positively correlated. Together, these results suggest that changes in cortical excitability in opposite directions lead to corresponding changes in local sleep regulation, as reflected by SWA, providing evidence for a tight relationship between cortical plasticity and sleep intensity." ]
H9N2 avian influenza virus (AIV): a human pandemic threat	Poultry-adapted H9N2 avian influenza viruses (AIVs) are commonly found in many countries in Asia, the Middle East, Africa, and Europe, and although classified as low pathogenic viruses, they are an economically important disease. Besides the importance of the disease in the poultry industry, some H9N2 AIVs are also known to be zoonotic. The disease in humans appears to cause primarily a mild upper respiratory disease, and doesn't cause or only rarely causes the severe pneumonia often seen with other zoonotic AIVs like H5N1 or H7N9. Serologic studies in humans, particularly in occupationally exposed workers, show a large number of people with antibodies to H9N2, suggesting infection is commonly occurring. Of the four defined H9N2 poultry lineages, only two lineages, the G1 and the Y280 lineages, are associated with human infections. Almost all of the viruses from humans have a leucine at position 226 (H3 numbering) of the hemagglutinin associated with a higher affinity of binding with α2,6 sialic acid, the host cell receptor most commonly found on glycoproteins in the human upper respiratory tract. For unknown reasons there has also been a shift in recent years of poultry viruses in the G1 and Y280 lineages to also having leucine instead of glutamine, the amino acid found in most avian viruses, at position 226. The G1 and Y280 poultry lineages because of their known ability to infect humans, the high prevalence of the virus in poultry in endemic countries, the lack of antibody in most humans, and the shift of poultry viruses to more human-like receptor binding makes these viruses a human pandemic threat. Increased efforts for control of the virus, including through effective vaccine use in poultry, is warranted for both poultry and public health goals.	[ "H9N2 influenza A viruses are currently widespread in chickens, quail, and other poultry in Asia and have caused a few cases of influenza in humans. In this study, we found that H9N2 viruses from Hong Kong live bird markets have receptor specificity similar to that of human H3N2 viruses. In addition, the neuraminidase of poultry H9N2 viruses has mutations in its hemadsorbing site, a characteristic resembling that of human H2N2 and H3N2 viruses but differing from that of other avian viruses. Peculiar features of surface glycoproteins of H9N2 viruses from Hong Kong suggest an enhanced propensity for introduction into humans and emphasize the importance of poultry in the zoonotic transmission of influenza viruses.", "The first documented outbreak of human respiratory disease caused by avian influenza A (H5N1) viruses occurred in Hong Kong in 1997. The kinetics of the antibody response to the avian virus in H5N1-infected persons was similar to that of a primary response to human influenza A viruses; serum neutralizing antibody was detected, in general, >/=14 days after symptom onset. Cohort studies were conducted to assess the risk of human-to-human transmission of the virus. By use of a combination of serologic assays, 6 of 51 household contacts, 1 of 26 tour group members, and none of 47 coworkers exposed to H5N1-infected persons were positive for H5 antibody. One H5 antibody-positive household contact, with no history of poultry exposure, provided evidence that human-to-human transmission of the avian virus may have occurred through close physical contact with H5N1-infected patients. In contrast, social exposure to case patients was not associated with H5N1 infection.", "In parts of southern China, some large-scale swine farms are adjacent to lakes and ponds that are home to many types of birds. Some swine farms will also raise poultry for consumption and sale. Swine farms in rural China may be the source of the AIV outbreak. A seroepidemiological study was conducted among swine farm residents to understand the prevalence of antibodies against avian influenza virus (AIV) H9N2 in southern China. A total of 2,006 swine farm residents were sampled. Serum samples were tested for the presence of antibodies against H9N2 AIV by hemagglutination inhibition (HI) and microneutralization assays. A total of 37 serum samples from swine farm residents were HI positive for A/chicken/Guangdong/V/2008(H9N2), and 24 serum samples (all of which were also HI positive) were microneutralization assays positive for A/chicken/Guangdong/V/2008(H9N2). Due to the special pig farming model in southern China, the residents are in close contact with different kinds of birds. Thus, controlling bird-to-human transmission of AIV in swine farms with poultry may be an important means of preventing widespread AIV infection in humans.", "We report the clinical features of two cases of human infection with influenza A virus subtype H9N2 in Hong Kong, and show that serum samples from blood donors in Hong Kong had neutralising antibody suggestive of prior infection with influenza H9N2.", "Pandemic strains of influenza A virus arise by genetic reassortment between avian and human viruses. To examine the possibility that pigs serve as \"mixing vessels\" for such reassortment events (Scholtissek et al., Virology 147, 287-294, 1985), we phylogenetically analyzed the internal protein genes of classic H1N1, avian-like H1N1, and human-like H3N2 viruses circulating among Italian pigs. The results show that human-like H3N2 strains isolated from 1985 to 1989 contained the internal protein genes of avian-like H1N1 viruses, whereas those isolated in 1977 and 1983 did not. Thus, at some time between 1983 and 1985, genetic reassortment took place between avian- and human-like viruses in Italian pigs. This study provides the first evidence supporting genetic reassortment between human and avian viruses in a natural swine environment.", "Pigs are permissive to both human and avian influenza viruses and have been proposed to be an intermediate host for the genesis of pandemic influenza viruses through reassortment or adaptation of avian viruses. Prospective virological surveillance carried out between March 1998 and June 2000 in Hong Kong, Special Administrative Region, People's Republic of China, on pigs imported from southeastern China, provides the first evidence of interspecies transmission of avian H9N2 viruses to pigs and documents their cocirculation with contemporary human H3N2 (A/Sydney/5/97-like, Sydney97-like) viruses. All gene segments of the porcine H9N2 viruses were closely related to viruses similar to chicken/Beijing/1/94 (H9N2), duck/Hong Kong/Y280/97 (H9N2), and the descendants of the latter virus lineage. Phylogenetic analysis suggested that repeated interspecies transmission events had occurred from the avian host to pigs. The Sydney97-like (H3N2) viruses isolated from pigs were related closely to contemporary human H3N2 viruses in all gene segments and had not undergone genetic reassortment. Cocirculation of avian H9N2 and human H3N2 viruses in pigs provides an opportunity for genetic reassortment leading to the emergence of viruses with pandemic potential.", "The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics." ]
Establishment of a stable lentiviral expression vector for enhanced green fluorescent protein and evaluation of biological characteristics on HCC growth and migration following transfection of HCC cells with EGFP	Hepatocellular carcinoma (HCC), the most common primary tumor of the liver, has a poor prognosis, rapid progression. The aim of the current study was to establish a stable lentiviral expression vector for enhanced green fluorescent protein (EGFP) and to evaluate biological characteristics on HCC growth and migration following transfection of HCC cells with EGFP. McA-RH7777 cells were transfected with EGFP overexpression lentiviral vector. Cell activity and mobility were monitored with a Cell-IQ Analyzer. Transwell assays were performed to detect invasiveness and flow cytometry was performed for cell cycle analysis. A subcutaneous tumor rat model was established to analyze the stability of fluorescent protein expression. The result suggested no significant differences between wild-type and EGFP-overexpressing McA-RH7777 cells with regards to cell proliferation, activity, mobility, invasiveness and cell cycle. Green fluorescence was detected over 108 days of culturing. The subcutaneous tumor rat model demonstrated that EGFP expression had no influence on tumor growth and long-term expression was stable. The stable EGFP expression of the HCC transplanted tumor rat model may share biological characteristics with human liver cancer. The model established in the current study may be suitable for various applications, including research focusing on liver cancer metastasis and recurrence, interventional therapy, imaging diagnosis and drug screenings.	[ "Hemothorax caused by metastasis or direct invasion of hepatocellular carcinoma (HCC) in the chest is rare. We report a case of hemothorax caused by metastasis in the mediastinum and treated with transcatheter arterial embolization (TAE). A 60-year-old woman with HCC was admitted to receive chemotherapy. Two days after admission, she complained of dyspnea, and a chest X-ray revealed right pleural effusion. Thoracentesis confirmed the diagnosis of hemothorax. Computed tomography (CT) angiography showed lung, pleural, and mediastinal metastases and contrast extravasation from the right lower mediastinal mass. Hemothorax caused by spontaneous rupture of mediastinal metastasis of hepatocellular carcinoma. During emergent angiography, contrast extravasation from the right T10 intercostal artery was observed and we performed embolization with lipiodol and gelatin sponge particles. After embolization, no active bleeding was observed. The patient died because of sepsis and multiple organ failure 22 days after admission. We reviewed 21 cases of HCC with metastasis or direct invasion in the chest presenting hemothorax. The results revealed that male sex and right hemothorax were predominant in these cases. The average age of the patients was 61.24±10.82 years. The most common symptoms were dyspnea, chest wall pain, and shock. Thoracentesis can confirm the diagnosis, and CT angiography can help identify the location of contrast extravasation before TAE. The reported bleeding arteries were the intercostal, inferior phrenic, bronchial, hepatic, and superficial cervical arteries. TAE with embolic agents is a feasible treatment. The overall outcomes in these cases were poor.", "Multicolored proteins have allowed the color-coding of cancer cells growing in vivo and enabled the distinction of host from tumor with single-cell resolution. Non-invasive imaging with fluorescent proteins enabled the dynamics of metastatic cancer to be followed in real time in individual animals. Non-invasive imaging of cancer cells expressing fluorescent proteins has allowed the real-time determination of efficacy of candidate antitumor and antimetastatic agents in mouse models. The use of fluorescent proteins to differentially label cancer cells in the nucleus and cytoplasm can visualize the nuclear-cytoplasmic dynamics of cancer cells in vivo including: mitosis, apoptosis, cell-cycle position, and differential behavior of nucleus and cytoplasm that occurs during cancer-cell deformation and extravasation. Recent applications of the technology described here include linking fluorescent proteins with cell-cycle-specific proteins such that the cells change color from red to green as they transit from G1 to S phases. With the macro- and micro-imaging technologies described here, essentially any in vivo process can be imaged, giving rise to the new field of in vivo cell biology using fluorescent proteins.", "Reelin is a regulator of cell migration in the nervous system, and has other functions in the development of a number of non-neuronal tissues. In addition, alterations in reelin expression levels have been reported in breast, pancreatic, liver, gastric, and other cancers. Reelin is normally expressed in mammary gland stromal cells, but whether stromal reelin contributes to breast cancer progression is unknown. Herein, we used a syngeneic mouse mammary tumor transplantation model to examine the impact of host-derived reelin on breast cancer progression. We found that transplanted syngeneic tumors grew more slowly in reelin-deficient (rl Orl -/- ) mice and had delayed metastatic colonization of the lungs. Immunohistochemistry of primary tumors revealed that tumors grown in rl Orl -/- animals had fewer blood vessels and increased macrophage infiltration. Gene expression studies from tumor tissues indicate that loss of host-derived reelin alters the balance of M1- and M2-associated macrophage markers, suggesting that reelin may influence the polarization of these cells. Consistent with this, rl Orl -/- M1-polarized bone marrow-derived macrophages have heightened levels of the M1-associated cytokines iNOS and IL-6. Based on these observations, we propose a novel function for the reelin protein in breast cancer progression.", "We have established a line of transgenic mice expressing the A. victoria green fluorescent protein (GFP) under the control of the promoter for vascular endothelial growth factor (VEGF). Mice bearing the transgene show green cellular fluorescence around the healing margins and throughout the granulation tissue of superficial ulcerative wounds. Implantation of solid tumors in the transgenic mice leads to an accumulation of green fluorescence resulting from tumor induction of host VEGF promoter activity. With time, the fluorescent cells invade the tumor and can be seen throughout the tumor mass. Spontaneous mammary tumors induced by oncogene expression in the VEGF-GFP mouse show strong stromal, but not tumor, expression of GFP. In both wound and tumor models the predominant GFP-positive cells are fibroblasts. The finding that the VEGF promoter of nontransformed cells is strongly activated by the tumor microenvironment points to a need to analyze and understand stromal cell collaboration in tumor angiogenesis.", "To noninvasively image cancer cell/stromal cell interaction in the tumor microenvironment and drug response at the cellular level in live animals in real time, we developed a new imageable three-color animal model. The model consists of green fluorescent protein (GFP)-expressing mice transplanted with dual-color cancer cells labeled with GFP in the nucleus and red fluorescent protein in the cytoplasm. The Olympus IV100 Laser Scanning Microscope, with ultra-narrow microscope objectives (\"stick objectives\"), is used for three-color whole-body imaging of the two-color cancer cells interacting with the GFP-expressing stromal cells. In this model, drug response of both cancer and stromal cells in the intact live animal is also imaged in real time. Various in vivo phenomena of tumor-host interaction and cellular dynamics were imaged, including mitotic and apoptotic tumor cells, stromal cells interacting with the tumor cells, tumor vasculature, and tumor blood flow. This new model system enables the first cellular and subcellular images of unperturbed tumors in the live intact animal. New visible real-time targets for novel anticancer agents are provided in this model, including the color-coded interacting cancer and stromal cells, tumor vasculature, and blood flow. This imageable model should lead to many new insights of in vivo cancer cell biology and to novel drug discovery.", "Cancer surgery requires the complete and precise identification of malignant tissue margins including the smallest disseminated lesions. Internal green fluorescent protein (GFP) fluorescence can intensely illuminate even single cells but requires GFP sequence transcription within the cell. Introducing and selectively activating the GFP gene in malignant tissue in vivo is made possible by the development of OBP-401, a telomerase-dependent, replication-competent adenovirus expressing GFP. This potentially powerful adjunct to surgical navigation was demonstrated in 2 nude mouse models that represent difficult surgical challenges--the resection of widely disseminated cancer. HCT-116, a model of intraperitoneal disseminated human colon cancer, was labeled by virus injection into the peritoneal cavity. A549, a model of pleural dissemination of human lung cancer, was labeled by virus administered into the pleural cavity. Only the malignant tissue fluoresced brightly in both models. In the intraperitoneal model of disseminated cancer, fluorescence-guided surgery enabled resection of all tumor nodules labeled with GFP by OBP-401. The data in this report suggest that adenoviral-GFP labeling tumors in patients can enable fluorescence-guided surgical navigation.", "In this study, we examined the hypothesis that early pulmonary metastases form within the vasculature. We introduced primary tumors in immunocompromised mice by subcutaneous injection of murine breast carcinoma cells (4T1) expressing green fluorescent protein. Isolated ventilated and perfused lungs from these mice were examined at various times after tumor formation by fluorescent microscopy. The vasculature was visualized by counterstaining with 1,1-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine (DiI)-acetylated low-density lipoprotein. These experiments showed that metastatic cells derived by spontaneous metastases were intravascular, and that early colony formation was intravascular. The location of the tumor cells was confirmed by deconvolution analysis. This work extends our previous study(1) that sarcoma cells injected intravenously form intravascular colonies to spontaneous metastasis and to a carcinoma model system. Many of the tumor cells seen were single implying that tumor cells may travel as single cells. These results support a model for pulmonary metastasis in mice in which 1) tumor cells can attach to lung endothelium soon after arrival; 2) surviving tumor cells proliferate intravascularly in this model; and 3) extravasation of the tumor occurs when intravascular micrometastatic foci outgrow the vessels they are in." ]
Development of a comprehensive medical imaging application using HTML5 and WebGL	Despite the fact that a large number of web applications are used in the medical community, there are still certain technological challenges that need to be addressed, for example, browser plug-ins and efficient 3D visualization. These problems make it necessary for a specific browser plug-in to be preinstalled on the client side when launching applications. Otherwise, the applications fail to run due to the lack of the required software. This paper presents the latest techniques in hypertext markup language 5 (HTML5) and web graphics library (WebGL) for solving these problems and an evaluation of the suitability of the combination of HTML5 and WebGL for the development of web-based medical imaging applications. In this study, a comprehensive medical imaging application was developed using HTML5 and WebGL. This application connects to the medical image server, runs on a standard personal computer (PC), and is easily accessible via a standard web browser. The several functions required for radiological interpretation were implemented, for example, navigation, magnification, windowing, and fly-through. The HTML5-based medical imaging application was tested on major browsers and different operating systems over a local area network (LAN) and a wide area network (WAN). The experimental results revealed that this application successfully performed two-dimensional (2D) and three-dimensional (3D) functions on different PCs over the LAN and WAN. Moreover, it demonstrated an excellent performance for remote access users, especially over a short time period for 3D visualization and a real-time fly-through navigation. The results of the study demonstrate that HTML5 and WebGL combination is suitable for the development of medical imaging applications. Moreover, the advantages and limitations of these technologies are discussed in this paper.	[ "The vast amount of heterogeneous data generated in various fields of neurosciences such as neuropsychopharmacology can hardly be classified using traditional databases. We present here the concept of a virtual archive, spatially referenced over a simplified 3D brain map and accessible over the Internet. A simple prototype (available at http://aquatics.crs4.it/neuropsydat3d) has been realized using current Web-based virtual reality standards and technologies. It illustrates how primary literature or summary information can easily be retrieved through hyperlinks mapped onto a 3D schema while navigating through neuroanatomy. Furthermore, 3D navigation and visualization techniques are used to enhance the representation of brain's neurotransmitters, pathways and the involvement of specific brain areas in any particular physiological or behavioral functions. The system proposed shows how the use of a schematic spatial organization of data, widely exploited in other fields (e.g. Geographical Information Systems) can be extremely useful to develop efficient tools for research and teaching in neurosciences.", "To compare non-commercial DICOM toolkits for their de-identification ability in removing a patient's personal health information (PHI) from a DICOM header. Ten DICOM toolkits were selected for de-identification tests. Tests were performed by using the system's default de-identification profile and, subsequently, the tools' best adjusted settings. We aimed to eliminate fifty elements considered to contain identifying patient information. The tools were also examined for their respective methods of customization. Only one tool was able to de-identify all required elements with the default setting. Not all of the toolkits provide a customizable de-identification profile. Six tools allowed changes by selecting the provided profiles, giving input through a graphical user interface (GUI) or configuration text file, or providing the appropriate command-line arguments. Using adjusted settings, four of those six toolkits were able to perform full de-identification. Only five tools could properly de-identify the defined DICOM elements, and in four cases, only after careful customization. Therefore, free DICOM toolkits should be used with extreme care to prevent the risk of disclosing PHI, especially when using the default configuration. In case optimal security is required, one of the five toolkits is proposed. • Free DICOM toolkits should be carefully used to prevent patient identity disclosure. • Each DICOM tool produces its own specific outcomes from the de-identification process. • In case optimal security is required, using one DICOM toolkit is proposed.", "The digital imaging and communications in medicine (DICOM) protocol is the leading standard for image data management in healthcare. Imaging biomarkers and image-based surrogate endpoints in clinical trials and medical registries require DICOM viewer software with advanced functionality for visualization and interfaces for integration. In this paper, a comprehensive evaluation of 28 DICOM viewers is performed. The evaluation criteria are obtained from application scenarios in clinical research rather than patient care. They include (i) platform, (ii) interface, (iii) support, (iv) two-dimensional (2D), and (v) three-dimensional (3D) viewing. On the average, 4.48 and 1.43 of overall 8 2D and 5 3D image viewing criteria are satisfied, respectively. Suitable DICOM interfaces for central viewing in hospitals are provided by GingkoCADx, MIPAV, and OsiriX Lite. The viewers ImageJ, MicroView, MIPAV, and OsiriX Lite offer all included 3D-rendering features for advanced viewing. Interfaces needed for decentral viewing in web-based systems are offered by Oviyam, Weasis, and Xero. Focusing on open source components, MIPAV is the best candidate for 3D imaging as well as DICOM communication. Weasis is superior for workflow optimization in clinical trials. Our evaluation shows that advanced visualization and suitable interfaces can also be found in the open source field and not only in commercial products.", "Healthcare institutions are increasingly turning to digital medical imaging systems to promote better diagnosis and treatment of their patients. The implementation of the Picture Archiving and Communication System (PACS) clearly contributes to an increase in the productivity of health professionals. However, despite the amount of research that has been done in the past two decades, there are still several technological hurdles that hinder the wide adoption of PACS in the Web environment. In this paper, we present a Web-enabled PACS that through the inclusion of several DICOM services and compression methods promotes medical image availability and greater accessibility to users.", "Clinical research studies offer many challenges for their supporting information systems. AIBL assembled 1112 participants who volunteered crucial information for a comprehensive study on neurodegenerative diseases. This paper discusses the shortcomings of the clinical trial management system chosen to record the results of the study. A set of guidelines was devised and a critique of five systems ensued. OpenClinica was selected as the most appropriate option. The main contribution of this paper is: (i) proposing a set of guidelines to determine the appropriateness of Clinical Trial Management Systems (CTMS) solution; (ii) providing a brief critique of existing commercial and open-sourced CTMS; and (iii) alluding to some data migration issues and providing cues on how to address them. We conclude that open-source CTMS are viable alternatives to the more expensive commercial systems to conduct, record and manage clinical studies.", "Data sharing is increasingly recognized as critical to cross-disciplinary research and to assuring scientific validity. Despite National Institutes of Health and National Science Foundation policies encouraging data sharing by grantees, little data sharing of clinical data has in fact occurred. A principal reason often given is the potential of inadvertent violation of the Health Insurance Portability and Accountability Act privacy regulations. While regulations specify the components of private health information that should be protected, there are no commonly accepted methods to de-identify clinical data objects such as images. This leads institutions to take conservative risk-averse positions on data sharing. In imaging trials, where images are coded according to the Digital Imaging and Communications in Medicine (DICOM) standard, the complexity of the data objects and the flexibility of the DICOM standard have made it especially difficult to meet privacy protection objectives. The recent release of DICOM Supplement 142 on image de-identification has removed much of this impediment. This article describes the development of an open-source software suite that implements DICOM Supplement 142 as part of the National Biomedical Imaging Archive (NBIA). It also describes the lessons learned by the authors as NBIA has acquired more than 20 image collections encompassing over 30 million images.", "Clinical imaging data are essential for developing research software for computer-aided diagnosis, treatment planning and image-guided surgery, yet existing systems are poorly suited for data sharing between healthcare and academia: research systems rarely provide an integrated approach for data exchange with clinicians; hospital systems are focused towards clinical patient care with limited access for external researchers; and safe haven environments are not well suited to algorithm development. We have established GIFT-Cloud, a data and medical image sharing platform, to meet the needs of GIFT-Surg, an international research collaboration that is developing novel imaging methods for fetal surgery. GIFT-Cloud also has general applicability to other areas of imaging research. GIFT-Cloud builds upon well-established cross-platform technologies. The Server provides secure anonymised data storage, direct web-based data access and a REST API for integrating external software. The Uploader provides automated on-site anonymisation, encryption and data upload. Gateways provide a seamless process for uploading medical data from clinical systems to the research server. GIFT-Cloud has been implemented in a multi-centre study for fetal medicine research. We present a case study of placental segmentation for pre-operative surgical planning, showing how GIFT-Cloud underpins the research and integrates with the clinical workflow. GIFT-Cloud simplifies the transfer of imaging data from clinical to research institutions, facilitating the development and validation of medical research software and the sharing of results back to the clinical partners. GIFT-Cloud supports collaboration between multiple healthcare and research institutions while satisfying the demands of patient confidentiality, data security and data ownership." ]
Host immune cell parameters in non-small-cell lung cancer	Characterization of host immune cell parameters prior to treatment is expected to identify biomarkers predictive of clinical outcome as well as to elucidate why some patients fail to respond to immunotherapy. We monitored blood immune cells from 58 patients with non-small- cell lung cancer (NSCLC) undergoing surgery of the primary tumor and from 50 age-matched healthy volunteers. Complete leukocyte blood count, the number of circulating dendritic cells (DC), HLA-DR	[ "Eleven prognostic factors were retrospectively analyzed in 270 newly diagnosed patients with advanced non-small-cell lung cancer including age, sex, performance status, histology, stage, smoking status, hemoglobin level, forced expiratory volume in one second (FEV1), weight loss >5% in 3 months preceding therapy, number of involved organs, and type of first-line chemotherapy. Response rate was 35.6%, and median survival was 8.2 months (95% CI, 7.8 to 8.7) for the whole group. Age ≤60 years (P = .016), FEV1 ≥ 2L (P = .03), and the use of platinum/docetaxel (P < .0001) were significantly associated with an improved survival. Histology did not affect outcome in the absence of targeted therapies.", "Myeloid-derived suppressor cells (MDSC) accumulate in the spleen and tumor bed during tumor growth. They contribute to the immune tolerance of cancer notably by inhibiting the function of CD8(+) T cells. Thus, their elimination may hamper tumor growth by enhancing antitumor T-cell functions. We have previously reported that some anticancer agents relied on T cell-dependent anticancer responses to achieve maximal efficacy. However, the effect of anticancer agents on MDSC has remained largely unexplored. In this study, we observed that gemcitabine and 5-fluorouracil (5FU) were selectively cytotoxic on MDSC. In vivo, the treatment of tumor-bearing mice with 5FU led to a major decrease in the number of MDSC in the spleens and tumor beds of animals whereas no significant effect on T cells, natural killer cells, dendritic cells, or B cells was noted. Interestingly, 5FU showed a stronger efficacy over gemcitabine to deplete MDSC and selectively induced MDSC apoptotic cell death in vitro and in vivo. The elimination of MDSC by 5FU increased IFN-gamma production by tumor-specific CD8(+) T cells infiltrating the tumor and promoted T cell-dependent antitumor responses in vivo. Altogether, these findings suggest that the antitumor effect of 5FU is mediated, at least in part, by its selective cytotoxic action on MDSC.", "Myeloid-derived suppressor cells (MDSC) have emerged as key immune modulators in various tumor models and human malignancies, but their characteristics in humans remain to be unequivocally defined. In this study, we have examined circulating CD14(+)HLA-DR(-/low) MDSC in 34 advanced malignant melanoma (MM) patients. Their frequency is significantly increased and associated with disease activity. Contrary to the common notion that MDSC are a heterogeneous population of exclusively immature cells, we find the coexpression of markers associated with mature phenotype. We show for the first time the overexpression of CD80, CD83, and DC-Sign in human MDSC. Further, increased levels of signal transducer and activator of transcription 3 (Stat3), an important regulator in MDSC development and function, were noted in MM-MDSC. Stat3 was altered toward an active, phosphorylated state in the HLA-DR(-) population of CD14(+) cells and was more reactive to activating stimuli in patients. Importantly, inhibition of Stat3 abolished their suppressive activity almost completely. The described MM-MDSC use arginase in conjunction with other yet undefined mechanisms to suppress CD4(+) and CD8(+) T cells. Several observations suggest a redox imbalance in MDSC and indicate an important role of Stat3-dependent oxidative stress in MDSC-mediated T-cell suppression. These results emphasize the diversity of MDSC in human cancer and provide potential targets for therapeutic interventions.", "The TroVax Renal Immunotherapy Survival Trial was a randomized, placebo-controlled phase III study that investigated whether modified vaccinia Ankara encoding the tumor antigen 5T4 (MVA-5T4) prolonged survival of patients receiving first-line standard-of-care (SOC) treatment for metastatic renal cell cancer. Patients with metastatic clear cell renal cancer, prior nephrectomy, and good or intermediate prognosis were randomized 1:1 to receive up to 13 immunizations of MVA-5T4/placebo in combination with either sunitinib, interleukin-2 or interferon-α. The primary end point was overall survival. Secondary end points included progression-free survival, overall response rate, and safety. Seven hundred thirty-three patients were recruited (365 MVA-5T4 and 368 placebo). Treatment arms were well balanced for SOC and prognosis. No significant difference in the incidence of adverse events or serious adverse events was observed. No significant difference in overall survival was evident in the two treatment arms (median 20.1 months MVA-5T4 versus 19.2 months placebo; P = 0.55). The magnitude of the 5T4-specific antibody response induced by vaccination with MVA-5T4 was associated with enhanced patient survival. Furthermore, exploratory analyses suggested a number of pretreatment hematologic factors that could identify patients who derive significant benefit from this vaccine. MVA-5T4 in combination with SOC was well tolerated, but no difference in survival was observed in the overall study population. Exploratory analyses indicate that there may be subsets of patients who could gain significant benefit from MVA-5T4, but such results would need to be confirmed in future randomized clinical studies.", "Several immune suppressive mechanisms that evade the host immune response have been described in patients with hepatocellular carcinoma (HCC); one of these mechanisms is expansion of myeloid-derived suppressor cells (MDSCs). MDSCs have been shown to inhibit T cell responses in tumor-bearing mice, but little is known about these cells in humans. Here, we have analyzed and characterized the effect of MDSCs on the innate immune system, in particular, their interaction with natural killer (NK) cells in patients with HCC. MDSCs from patients with HCC inhibited autologous NK cell cytotoxicity and cytokine secretion when cultured together in vitro. This suppression was dependent on cell contact, but did not rely on the arginase activity of MDSCs, which is a hallmark function of these cells. However, MDSC-mediated inhibition of NK cell function was dependent mainly on the NKp30 on NK cells. Our study suggests a new role for MDSCs in patients with HCC in disarming the innate immune system and further contributing to the immune suppressor network in these patients. These findings have important implications when designing immunotherapy protocols.", "Myeloid cells are the most abundant nucleated haematopoietic cells in the human body and are a collection of distinct cell populations with many diverse functions. The three groups of terminally differentiated myeloid cells - macrophages, dendritic cells and granulocytes - are essential for the normal function of both the innate and adaptive immune systems. Mounting evidence indicates that the tumour microenvironment alters myeloid cells and can convert them into potent immunosuppressive cells. Here, we consider myeloid cells as an intricately connected, complex, single system and we focus on how tumours manipulate the myeloid system to evade the host immune response.", "The association between malignancy and development of a paraneoplastic leukocytosis, the so-called leukemoid reaction, has long been appreciated. Although a leukemoid reaction has conventionally been defined as a peripheral blood leukocytosis composed of both mature and immature granulocytes that exceeds 50,000/microL, a less profound leukocytosis may be appreciated in many patients harboring a malignant disease. More recent insights have shed new light on this long-recognized association, because research performed in both murine models and cancer patients has uncovered multiple mechanisms by which tumors both drive myelopoiesis, sometimes leading to a clinically apparent leukocytosis, and inhibit the differentiation of myeloid cells, resulting in a qualitative change in myelopoiesis. This qualitative change leads to the accumulation of immature myeloid cells, which due to their immune suppressive effects have been collectively called myeloid-derived suppressor cells. More recently, myeloid cells have been shown to promote tumor angiogenesis. Cancer-associated myeloproliferation is not merely a paraneoplastic phenomenon of questionable importance but leads to the suppression of host immunity and promotion of tumor angiogenesis, both of which play an integral part in tumorigenesis and metastasis. Therefore, cancer-associated myeloproliferation represents a novel therapeutic target in cancer that, decades after its recognition, is only now being translated into clinical practice.", "Tumors escape immune recognition by several mechanisms, and induction of myeloid derived suppressor cells (MDSC) is thought to play a major role in tumor mediated immune evasion. MDSC arise from myeloid progenitor cells that do not differentiate into mature dendritic cells, granulocytes, or macrophages, and are characterized by the ability to suppress T cell and natural killer cell function. They are increased in patients with cancer including renal cell carcinoma (RCC), and their levels have been shown to correlate with prognosis and overall survival. Multiple methods of inhibiting MDSCs are currently under investigation. These can broadly be categorized into methods that (a) promote differentiation of MDSC into mature, non-suppressive cells (all trans retinoic acid, vitamin D), (b) decrease MDSC levels (sunitinib, gemcitabine, 5-FU, CDDO-Me), or (c) functionally inhibit MDSC (PDE-5 inhibitors, cyclooxygenase 2 inhibitors). Recently, several pre-clinical tumor models of combination therapy involving sunitinib plus vaccines and/or adoptive therapy have shown promise in MDSC inhibition and improved outcomes in the tumor bearing host. Current clinical trials are underway in RCC patients to assess not only the impact on clinical outcome, but how this combination can enhance anti-tumor immunity and reduce immune suppression. Decreasing immune suppression by MDSC in the cancer host may improve outcomes and prolong survival in this patient population.", "Inflammation is a critical component of normal tissue repair, as well as being fundamental to the body's defense against infection. Environmental factors, such as smoking, have been reported to modify the host response and hence modify inflammation progression, severity and outcome. Therefore, a comprehensive understanding of the molecular mechanisms by which smoking affects inflammation is vital for preventive and therapeutic strategies on a clinical level. The purpose of the present article is to review the potential biological mechanisms by which smoking affects inflammation, emphasizing recent developments. Smoking is reported to effect a number of biological mediators of inflammation through its effect on immune-inflammatory cells, leading to an immunosuppressant state. Recent evidence strongly suggests that the molecular mechanisms behind the modulation of inflammation by smoking mainly involve the nuclear factor-kappa B (NF-kB) family, through the activation of both an inhibitor of IkB kinase (IKK)-dependent and -independent pathway. In addition to NF-kB activation, a number of transcriptional factors including GATA, PAX5 and Smad 3/4, have also been implicated. Multiple mechanisms may be responsible for the association of smoking and inflammation, and the identification of potential therapeutic targets should guide future research.", "Active suppression of tumor-specific T lymphocytes can limit the immune-mediated destruction of cancer cells. Of the various strategies used by tumors to counteract immune attacks, myeloid suppressors recruited by growing cancers are particularly efficient, often resulting in the induction of systemic T lymphocyte dysfunction. We have previously shown that the mechanism by which myeloid cells from tumor-bearing hosts block immune defense strategies involves two enzymes that metabolize L-arginine: arginase and nitric oxide (NO) synthase. NO-releasing aspirin is a classic aspirin molecule covalently linked to a NO donor group. NO aspirin does not possess direct antitumor activity. However, by interfering with the inhibitory enzymatic activities of myeloid cells, orally administered NO aspirin normalized the immune status of tumor-bearing hosts, increased the number and function of tumor-antigen-specific T lymphocytes, and enhanced the preventive and therapeutic effectiveness of the antitumor immunity elicited by cancer vaccination. Because cancer vaccines and NO aspirin are currently being investigated in independent phase I/II clinical trials, these findings offer a rationale to combine these treatments in subjects with advanced neoplastic diseases." ]
Inactivated NNA venom proteins in hens immunized with cobra venom proteins	Traditional, horse-derived antivenin is currently the most efficient treatment against snake bites. However, it is costly and has unpredictable side effects. Thus, alternative, cost-effective strategies for producing antivenin are needed. In this study, we immunized hens with inactivated NNA venom proteins from the cobra	[ "It was previously reported that up-regulation of alpha-enolase protein was detected in 65% of patients with non-small cell lung cancers (NSCLC). Moreover, a high titer of anti-alpha-enolase antibodies was developed in a smaller proportion (7.4%) of these patients than in non-tumor-associated patients and healthy subjects. In the present study, we characterized polyclonal and single-chain variable fragment (scFv) anti-alpha-enolase antibodies from immunized chickens. The E. coli-derived recombinant alpha-enolase protein was purified to its high homogenicity as verified by SDS-PAGE. After the 4th immunization, a high titer of specific polyclonal anti-alpha-enolase antibodies was elicited in immunized chickens and specifically recognized the purified human alpha-enolase antigen as determined by Western blot and ELISA. The expressed heavy and light chain variable genes (VH and VL) were isolated from spleen B cells and amplified to construct phage antibody libraries containing scFv molecules. After four rounds of panning selection, the scFv antibodies of randomly chosen clones were expressed and their binding specificity to alpha-enolase protein was verified using competitive ELISA, flow cytometry and immunofluorescence staining. Nucleotide sequence analysis from 10 alpha-enolase binding clones showed that 3 (30%) clones used identical heavy and light genes for scFv antibody expression, as represented by EnL5. Notably, amino acid changes in complementarity-determining regions (CDRs) were more frequently observed than those in framework regions (FRs) in all clones, indicating a strong affinity selection through mutations. All together, it is believed that these polyclonal and scFv IgY antibodies may be helpful in the development of molecular diagnostic and therapeutic agents for lung cancers in the future.", "Small Cell Lung Cancer (SCLC), a clinically aggressive cancer, accounts for approximately 25% of primary lung cancers. We carried out suppression subtractive hybridization (SSH), a PCR-based method for cDNA subtraction, between the human classic, NCI-H69 and variant, more aggressive NCI-N417 SCLC cell lines to isolate and characterize variable expression of genes, which may be responsible for differential degree of tumorigenicity of SCLC. Using NCI-N417 as a tester, we obtained 28 differentially expressed cDNA clones from a total of 60 arbitrarily picked clones. Among the 28 cDNA clones, 4 were unknown genes, 2 were fatty acid binding protein (FABP) with specific identification of mRNA for mammary-derived growth inhibitor (MDGI), 1 was human alpha-enolase, 4 were ribosomal proteins, 2 were structural genes, vimentin and moesin (membrane-organizing extension spike protein), and 9 were homologous with murine leukemia viruses, whereas 2 others had enhanced expression in NCI-H69 and A549 cell lines, and 4 were cell surface proteins and murine type C retrovirus. Expression of FABP/MDGI was significantly high in NCI-H417, which may influence mitosis and cell growth as implicated in other tissues, contrary to the conclusion drawn for the role of MDGI in human breast cancer. Higher expression of ribosomal proteins in NCI-N417 compared to NCI-H69 may have a role in differential tumorigenicity and metastatic ability. Further, we obtained 14 differentially expressed cDNA clones by reversing the tester and driver, using NCI-H69 as a tester. Of these 14 differential cDNAs, 5 were unknown genes, 2 were specific for keratins, others had similarities with protease inhibitor, human BAC clone, Alu RNA binding protein, and tumor expression-enhanced gene. Characterization of these differentially expressed cDNA clones will provide useful information in understanding of the genes responsible for differential tumorigenicity of SCLC.", "In order to examine how tumorigenicity is abrogated by gap junctional intercellular communication (GJIC), protein expression was analyzed in four related mouse lung epithelial cell lines that vary in their GJIC status and neoplastic potential. Since alterations in protein expression underlie neoplastic behavior, this proteomic analysis provides insights into the molecular pathogenesis of lung cancer. E10, an immortalized but non-tumorigenic cell line derived from alveolar type II pneumocytes, has functional GJIC. E9, a spontaneous transformant of E10, is GJIC-deficient and is tumorigenic upon injection into a syngeneic mouse. Stable transfection of E9 with Gja1, the gene for the gap junctional protein, connexin 43, re-established GJIC and rendered this line (designated E9-2) non-tumorigenic; the vector transfection control line, E9-41, remains tumorigenic. Proteins extracted from these cell lines were separated by two-dimensional electrophoresis (2DE) and visualized by Coomassie blue staining. We consistently observed differential expression of 27 proteins between E10 and E9 and identified 11 of these by peptide mass mapping. The functions of these proteins include stress response, cytoskeletal structure, signal transduction, apoptosis, immune response, pre-mRNA processing, and carbohydrate metabolism. Gja1 transfection affected the concentrations of four of these proteins, viz. PDI, alpha-enolase, aldolase A, and gelsolin-like protein. PDI concentration was most profoundly affected; E10 cells contain twice as much PDI as E9, and PDI was restored to E10-like levels in the E9-2 transfectant line while remaining at E9-like levels in the vector control E9-41 cells. An association between connexin 43 and PDI expression was also observed in a second set of independently derived type II cell lines. The PDI superfamily has multiple cellular roles including chaperoning assembled glycoproteins, regulating the activities of transcription factors, and regulating disulfide bond formation.", "The use of egg yolk antibodies (IgY) instead of IgG from mammalian species may present several advantages in the development of routine diagnostic immunoassays. On the one hand, the animal suffering is reduced, as antibodies are obtained directly from the egg. On the other hand, the use of IgY avoids the rheumatoid factor interference. The rheumatoid factor interacts with IgG molecules in many immunoassays causing false positive results. Despite these advantages, IgY antibodies are scarcely used. As part of an aim to develop a diagnostic test based on IgY-latex agglutination, a preliminary study on some characteristics of the IgY-latex complexes is carried out. In this work, protein adsorption and desorption, isoelectric point, electrokinetic mobility, and colloidal stability are analysed. Results are compared to those obtained by IgG. Interesting differences are observed (which mainly arise from the difference in molecular structure between IgY and IgG), suggesting that IgY is a more hydrophobic molecule than IgG. In addition, colloidal dispersions of IgY-covered latex particles are more stable (at pH 8) than those sensitized by IgG.", "Two bluetongue virus (BTV) serotype 10-specific single-chain Fv chicken antibody fragments (scFvs) were evaluated in a competitive ELISA. The binding of one (F3) to purified BTV was only inhibited by antibodies against the homologous serotype. The binding of the other (F10) was blocked by antisera to each of the 24 BTV serotypes. F10 recognised VP7, a major structural protein of the BTV core, but not if the protein was directly adsorbed to a plastic surface. It did, however, bind to recombinant VP7 that had been captured from suspension by rabbit IgG. This made it possible to develop an scFv based inhibition ELISA for BTV antibodies using recombinant VP7 without prior purification. The resulting immunoassay detected antibodies to 24 BTV serotypes, but not those directed against three serotypes of the related epizootic haemorrhagic disease virus. A phage library displaying fusion peptides expressed by fragments of the BTV genome segment 7 cDNA was constructed and screened using F10. Comparing selected peptides with the amino acid sequence of VP7 showed that recognition by the scFv required at least 131 residues representing the protein's upper domain. By providing well-characterised immunological reagents, recombinant antibody technology can contribute to the development of improved immunoassays for BTV diagnosis.", "Tissue damage analysis by traditional laboratory techniques is problematic. Proteomic analysis of exudates collected from affected tissue constitutes a powerful approach to assess tissue alterations, since biomarkers associated with pathologies can be identified in very low concentrations. In this study we proteomically explore the pathological effects induced by the venom of the viperid snake Bothrops asper in the gastrocnemius muscle of mice. Predominant proteins identified in the exudates included intracellular proteins, plasma proteins, extracellular matrix proteins and cell membrane-associated proteins. The presence of such proteins indicates cytotoxicity, plasma exudation, extracellular matrix degradation and shedding of membrane proteins. Some of these proteins may represent useful biomarkers for myonecrosis and microvascular damage. The effect of fucoidan, an inhibitor of myotoxic phospholipases A(2), and batimastat, an inhibitor of metalloproteinases, on the pathological effects induced by B. asper venom were also investigated. Fucoidan reduced the presence of intracellular proteins in exudates, whereas batimastat reduced the amount of relevant extracellular matrix proteins. The combination of these inhibitors resulted in the abrogation of the most relevant pathological effects of this venom. Thus, proteomic analysis of exudates represents a valuable approach to assess the characteristics of tissue damage in pathological models and the success of therapeutic interventions.", "The alpha isoform of enolase is a candidate plasminogen receptor on U937 monocytoid cells [Miles, L. A., Dahlberg, C. L., Plescia, J., Felez, J., Kato, K. & Plow, E. F. (1991) Biochemistry 30, 1682-1691]. In the present study, an enolase-related molecule was detected on the surfaces of peripheral blood monocytes and neutrophils by fluorescence-activated cell sorting. A mRNA transcript encoding a unique membrane form of an enolase-related molecule was not detected by Northern-blotting and primer-extension analyses, consistent with the cell-surface protein being authentic alpha-enolase. Both the alpha and beta isoforms of purified enolase, bound plasminogen with an affinity similar to that of the cell surface. Moreover, immunopurified alpha-enolase enhanced plasminogen activation by tissue plasminogen activator and blocked the binding of plasminogen to alpha 2-antiplasmin, mimicking functions arising from the association of plasminogen with cells. The interaction of the enolase isoforms with plasminogen was dependent upon recognition of the C-terminal lysyl residue of the enolases by the lysine-binding sites of plasminogen, as the interaction was blocked by (a) peptides with C-terminal lysine residues and (b) an antibody to the C-terminal aspect of enolase. A monoclonal antibody was developed, characterized and utilized to quantify the enolase molecules present on the surface of U937 cells. A substantial number of molecules, 1.8 x 10(6)/cell, was present, accounting for approximately 10% of the plasminogen-binding capacity of these cells. These studies clearly establish the role of enolase as a cell-surface plasminogen-binding site with profibrinolytic functions." ]
Identification of plasma membrane proteins expressed by estrogen receptor -positive, HER2-positive and triple negative breast cancer cells	In recent years, there has been an emphasis on personalizing breast cancer treatment in order to avoid the debilitating side effects caused by broad-spectrum chemotherapeutic drug treatment. Development of personalized medicine requires the identification of proteins that are expressed by individual tumors. Herein, we reveal the identity of plasma membrane proteins that are overexpressed in estrogen receptor α-positive, HER2-positive, and triple negative breast cancer cells. The proteins we identified are involved in maintaining protein structure, intracellular homeostasis, and cellular architecture; enhancing cell proliferation and invasion; and influencing cell migration. These proteins may be useful for breast cancer detection and/or treatment.	[ "Sushi domain containing 2 (SUSD2) is type I membrane protein containing domains inherent to adhesion molecules. There have been few reported studies on SUSD2, and they have mainly focused on breast cancer, colon cancer, and HeLa cells. However, the expression and function of SUSD2 in other cancers remain unclear. In the present study, we conducted an integrated bioinformatics analysis based on the array data from the GEO database and found a significant downregulation of SUSD2 in renal cell carcinoma (RCC) and lung cancer. Western blotting and quantitative RT-PCR (qRT-PCR) confirmed that SUSD2 was frequently decreased in RCC and lung cancer tissues compared with the corresponding levels in normal adjacent tissues. The restoration of SUSD2 expression inhibited the proliferation and clonogenicity of RCC and lung cancer cells, whereas the knockdown of SUSD2 promoted A549 cell growth. Our findings suggested that SUSD2 functions as a tumor suppressor gene (TSG) in RCC and lung cancer.", "Despite the involvement of the elongation factors eEF1A (eEF1A1 and eEF1A2) in the development of different cancers no information is available on their possible contribution to the biology of hepatocellular carcinoma (HCC). We investigated the expression of both forms of eEF1A in HepG2 and JHH6 cell lines considered to be a good in vitro model of HCC at different stage of differentiation. Our data indicate that the mRNA amount of eEF1A1 is increased in both cell lines as compared to normal liver tissue, but eEF1A2 mRNA level is markedly increased only in JHH6. Moreover, the less differentiated cell line JHH6 displays higher EEF1A1 and EEF1A2 mRNAs levels and an higher nuclear-enriched/cytoplasm ratio of EEF1A protein compared to the better differentiated HepG2 cell line. Over-expression depends only partially on gene amplification. The more abundant mRNA levels and the higher nuclear-enriched/cytoplasm ratio of eEF1A in JHH6 neither correlate with apoptosis resistance nor with proliferation rate in sub-confluent cells. However, in confluent cells, a clear tendency to maintain JHH6 into the cell cycle was observed. In conclusion, we document the increased mRNA levels of EEF1A genes in HCC cell lines compared to normal liver. Additionally, we show the increased nuclear-enriched/cytoplasmic protein ratio of eEF1A and the marked raise of the expression of both eEF1A forms in JHH6 compared to HepG2, suggesting the possibility that eEF1A forms might become a relevant markers related to HCC tumor phenotype.", "Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide and is characterized by aggressive tumor behavior coupled with poor prognosis. Various etiologies have been linked to HCC development, most prominently chronic hepatitis B and C virus infections as well as chronic alcohol consumption. In approximately 10% of HCCs, the etiology remains cryptic; however, recent epidemiological data suggest that most of these cryptogenic HCCs develop due to nonalcoholic steatohepatitis. To identify etiology-dependent DNA copy number aberrations and genes relevant to hepatocarcinogenesis, we performed array-based comparative genomic hybridization of 63 HCCs of well-defined etiology and 4 HCC cell lines followed by gene expression profiling and functional analyses of candidate genes. For a 10-megabase chromosome region on 8q24, we observed etiology-dependent copy number gains and MYC overexpression in viral and alcohol-related HCCs, resulting in up-regulation of MYC target genes. Cryptogenic HCCs showed neither 8q24 gains, nor MYC overexpression, nor target gene activation, suggesting that tumors of this etiology develop by way of a distinct MYC-independent pathomechanism. Furthermore, we detected several etiology-independent small chromosome aberrations, including amplification of MDM4 on 1q32.1 and frequent gains of EEF1A2 on 20q13.33. Both genes were overexpressed in approximately half the HCCs examined, and gene silencing reduced cell viability as well as proliferation and increased apoptosis rates in HCC cell lines. Our findings suggest that MDM4 and EEF1A2 act as etiology-independent oncogenes in a significant percentage of HCCs.", "Oestrogen receptor-α (ER) is the defining and driving transcription factor in the majority of breast cancers and its target genes dictate cell growth and endocrine response, yet genomic understanding of ER function has been restricted to model systems. Here we map genome-wide ER-binding events, by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq), in primary breast cancers from patients with different clinical outcomes and in distant ER-positive metastases. We find that drug-resistant cancers still recruit ER to the chromatin, but that ER binding is a dynamic process, with the acquisition of unique ER-binding regions in tumours from patients that are likely to relapse. The acquired ER regulatory regions associated with poor clinical outcome observed in primary tumours reveal gene signatures that predict clinical outcome in ER-positive disease exclusively. We find that the differential ER-binding programme observed in tumours from patients with poor outcome is not due to the selection of a rare subpopulation of cells, but is due to the FOXA1-mediated reprogramming of ER binding on a rapid timescale. The parallel redistribution of ER and FOXA1 binding events in drug-resistant cellular contexts is supported by histological co-expression of ER and FOXA1 in metastatic samples. By establishing transcription-factor mapping in primary tumour material, we show that there is plasticity in ER-binding capacity, with distinct combinations of cis-regulatory elements linked with the different clinical outcomes.", "Transcriptomic screens in breast cancer cell lines have identified a protein named anterior gradient-2 (AGR2) as a potentially novel oncogene overexpressed in estrogen receptor (ER) positive tumours. As targeting the ER is responsible for major improvements in cure rates and prevention of breast cancers, we have evaluated the pro-oncogenic function of AGR2 in anti-hormone therapeutic responses. We show that AGR2 expression promotes cancer cell survival in clonogenic assays and increases cell proliferation and viability in a range of cancer cell lines. Chromatin immunoprecipitation and reporter assays indicate that AGR2 is transcriptionally activated by estrogen through ERalpha. However, we also found that AGR2 expression is elevated rather than inhibited in response to tamoxifen, thus identifying a novel mechanism to account for an agonistic effect of the drug on a specific pro-oncogenic pathway. Consistent with these data, clinical analysis indicates that AGR2 expression is related to treatment failure in ERalpha-positive breast cancers treated with tamoxifen. In contrast, AGR2 is one of the most highly suppressed genes in cancers of responding patients treated with the anti-hormonal drug letrozole. These data indicate that the AGR2 pathway represents a novel pro-oncogenic pathway for evaluation as anti-cancer drug developments, especially therapies that by-pass the agonist effects of tamoxifen.", "Agr2 is a putative protein disulfide isomerase (PDI) initially identified as an estrogen-responsive gene in breast cancer cell lines. While Agr2 expression in breast cancer is positively correlated with estrogen receptor (ER) expression, it is upregulated in both hormone dependent and independent carcinomas. Several in vitro and xenograft studies have implicated Agr2 in different oncogenic features of breast cancer; however, the physiological role of Agr2 in normal mammary gland development remains to be defined. Agr2 expression is developmentally regulated in the mammary gland, with maximum expression during late pregnancy and lactation. Using a mammary gland specific knockout mouse model, we show that Agr2 facilitates normal lobuloalveolar development by regulating mammary epithelial cell proliferation; we found no effects on apoptosis in Agr2(-/-) mammary epithelial cells. Consequently, mammary glands of Agr2(-/-) females exhibit reduced expression of milk proteins, and by two weeks post-partum their pups are smaller in size. Utilizing a conditional mouse model, we show that Agr2 constitutive expression drives precocious lobuloalveolar development and increased milk protein expression in the virgin mammary gland. In vitro studies using knock down and overexpression strategies in estrogen receptor positive and negative mammary epithelial cell lines demonstrate a role for Agr2 in estradiol-induced cell proliferation. In conclusion, the estrogen-responsive Agr2, a candidate breast cancer oncogene, regulates epithelial cell proliferation and lobuloalveolar development in the mammary gland. The pro-proliferative effects of Agr2 may explain its actions in early tumorigenesis.", "Alanine, serine, cysteine-preferring transporter 2 (ASCT2; SLC1A5) mediates uptake of glutamine, a conditionally essential amino acid in rapidly proliferating tumour cells. Uptake of glutamine and subsequent glutaminolysis is critical for activation of the mTORC1 nutrient-sensing pathway, which regulates cell growth and protein translation in cancer cells. This is of particular interest in breast cancer, as glutamine dependence is increased in high-risk breast cancer subtypes. Pharmacological inhibitors of ASCT2-mediated transport significantly reduced glutamine uptake in human breast cancer cell lines, leading to the suppression of mTORC1 signalling, cell growth and cell cycle progression. Notably, these effects were subtype-dependent, with ASCT2 transport critical only for triple-negative (TN) basal-like breast cancer cell growth compared with minimal effects in luminal breast cancer cells. Both stable and inducible shRNA-mediated ASCT2 knockdown confirmed that inhibiting ASCT2 function was sufficient to prevent cellular proliferation and induce rapid cell death in TN basal-like breast cancer cells, but not in luminal cells. Using a bioluminescent orthotopic xenograft mouse model, ASCT2 expression was then shown to be necessary for both successful engraftment and growth of HCC1806 TN breast cancer cells in vivo. Lower tumoral expression of ASCT2 conferred a significant survival advantage in xenografted mice. These responses remained intact in primary breast cancers, where gene expression analysis showed high expression of ASCT2 and glutamine metabolism-related genes, including GLUL and GLS, in a cohort of 90 TN breast cancer patients, as well as correlations with the transcriptional regulators, MYC and ATF4. This study provides preclinical evidence for the feasibility of novel therapies exploiting ASCT2 transporter activity in breast cancer, particularly in the high-risk basal-like subgroup of TN breast cancer where there is not only high expression of ASCT2, but also a marked reliance on its activity for sustained cellular proliferation.", "We report that breast cancer cells that infiltrate the lungs support their own metastasis-initiating ability by expressing tenascin C (TNC). We find that the expression of TNC, an extracellular matrix protein of stem cell niches, is associated with the aggressiveness of pulmonary metastasis. Cancer cell-derived TNC promotes the survival and outgrowth of pulmonary micrometastases. TNC enhances the expression of stem cell signaling components, musashi homolog 1 (MSI1) and leucine-rich repeat-containing G protein-coupled receptor 5 (LGR5). MSI1 is a positive regulator of NOTCH signaling, whereas LGR5 is a target gene of the WNT pathway. TNC modulation of stem cell signaling occurs without affecting the expression of transcriptional enforcers of the stem cell phenotype and pluripotency, namely nanog homeobox (NANOG), POU class 5 homeobox 1 (POU5F1), also known as OCT4, and SRY-box 2 (SOX2). TNC protects MSI1-dependent NOTCH signaling from inhibition by signal transducer and activator of transcription 5 (STAT5), and selectively enhances the expression of LGR5 as a WNT target gene. Cancer cell-derived TNC remains essential for metastasis outgrowth until the tumor stroma takes over as a source of TNC. These findings link TNC to pathways that support the fitness of metastasis-initiating breast cancer cells and highlight the relevance of TNC as an extracellular matrix component of the metastatic niche.", "Although rapid signaling by estrogen at the plasma membrane is established, it is controversial as to the nature of the receptor protein. Estrogen may bind membrane proteins comparable to classical nuclear estrogen receptors (ERs), but some studies identify nonclassical receptors, such as G protein-coupled receptor (GPR)30. We took several approaches to define membrane-localized estrogen-binding proteins. In endothelial cells (ECs) from ERalpha/ERbeta combined-deleted mice, estradiol (E2) failed to specifically bind, and did not activate cAMP, ERK, or phosphatidyinositol 3-kinase or stimulate DNA synthesis. This is in contrast to wild-type ECs, indicating the lack of any functional estrogen-binding proteins in ERalpha/ERbeta combined-deleted ECs. To directly determine the identity of membrane and nuclear-localized ER, we isolated subcellular receptor pools from MCF7 cells. Putative ER proteins were trypsin digested and subjected to tandem array mass spectrometry. The output analysis identified membrane and nuclear E2-binding proteins as classical human ERalpha. We also determined whether GPR30 plays any role in E2 rapid actions. MCF7 (ER and GPR30 positive) and SKBR-3 (ER negative, GPR30 positive) cells were incubated with E2. Only MCF7 responded with significantly increased signaling. In MCF7, the response to E2 was not different in cells transfected with small interfering RNA to green fluorescent protein or GPR30. In contrast, interfering RNA to ERalpha or ER inhibition prevented rapid signaling and resulting biology in MCF7. In breast cancer and ECs, nuclear and membrane ERs are the same proteins. Furthermore, classical ERs mediate rapid signals induced by E2 in these cells.", "Human immunodeficiency virus type 1 (HIV-1) Nef-encoded protein plays key functions at almost all stages of the viral life cycle, but its role in translation is largely unknown. To determine the effect of Nef on translation we used an in vitro translation assay. The detection of Nef/RPS10 complexes and the presence of 18S rRNA and tRNAs in the complexes were performed by coimmunoprecipitation and RT-PCR assay. We observed that the HIV-1 Nef protein specifically impaired translation in vitro. We observed the interaction of Nef with RPS10 by coimmunoprecipitation assay. In addition 18S rRNA and tRNAs were present in the Nef/RPS10 complexes. Our results are consistent with a model in which the Nef protein by binding to two components of the 40S small ribosomal subunit, RPS10 and 18S rRNA, and to a lesser extent to tRNAs, could lead to decreased protein synthesis." ]
How do I get a list of all hypervirulents in a database?	Hypervirulent	[ "Klebsiella pneumoniae is an important cause of nosocomial Gram-negative sepsis. Lipopolysaccharide (LPS) is considered to be a major virulence determinant of this encapsulated bacterium and most mutations to the lipid A anchor of LPS are conditionally lethal to the bacterium. We studied the role of LPS acylation in K. pneumoniae disease pathogenesis by using a mutation of lpxM (msbB/waaN), which encodes the enzyme responsible for late secondary acylation of immature lipid A molecules. A K. pneumoniae B5055 (K2:O1) lpxM mutant was found to be attenuated for growth in the lungs in a mouse pneumonia model leading to reduced lethality of the bacterium. B5055DeltalpxM exhibited similar sensitivity to phagocytosis or complement-mediated lysis than B5055, unlike the non-encapsulated mutant B5055nm. In vitro, B5055DeltalpxM showed increased permeability of the outer membrane and an increased susceptibility to certain antibacterial peptides suggesting that in vivo attenuation may be due in part to sensitivity to antibacterial peptides present in the lungs of BALB/c mice. These data support the view that lipopolysaccharide acylation plays a important role in providing Gram-negative bacteria some resistance to structural and innate defenses and especially the antibacterial properties of detergents (e.g. bile) and cationic defensins.", "A new hypervirulent (hypermucoviscous) variant of Klebsiella pneumoniae has emerged. First described in the Asian Pacific Rim, it now increasingly recognized in Western countries. Defining clinical features are the ability to cause serious, life-threatening community-acquired infection in younger healthy hosts, including liver abscess, pneumonia, meningitis and endophthalmitis and the ability to metastatically spread, an unusual feature for enteric Gram-negative bacilli in the non-immunocompromised. Despite infecting a healthier population, significant morbidity and mortality occurs. Although epidemiologic features are still being defined, colonization, particularly intestinal colonization, appears to be a critical step leading to infection. However the route of entry remains unclear. The majority of cases described to date are in Asians, raising the issue of a genetic predisposition vs. geospecific strain acquisition. The traits that enhance its virulence when compared with \"classical\" K. pneumoniae are the ability to more efficiently acquire iron and perhaps an increase in capsule production, which confers the hypermucoviscous phenotype. An objective diagnostic test suitable for routine use in the clinical microbiology laboratory is needed. If/when these strains become increasingly resistant to antimicrobials, we will be faced with a frightening clinical scenario.", "Biofilm formation is a major virulence factor contributing to the chronicity of infections. To date few studies have evaluated biofilm formation in infecting isolates of patients including both Gram-positive and Gram-negative multidrug-resistant (MDR) species in the context of numerous types of infectious syndromes. Herein, we investigated the biofilm forming capacity in a large collection of single patient infecting isolates and compared the relationship between biofilm formation to various strain characteristics. The biofilm-forming capacity of 205 randomly sampled clinical isolates from patients, collected from various anatomical sites, admitted for treatment at Brooke Army Medical Center (BAMC) from 2004-2011, including methicillin-resistant/methicillin susceptible Staphylococcus aureus (MRSA/MSSA) (n=23), Acinetobacter baumannii (n=53), Pseudomonas aeruginosa (n=36), Klebsiella pneumoniae (n=54), and Escherichia coli (n=39), were evaluated for biofilm formation using the high-throughput microtiter plate assay and scanning electron microscopy (SEM). Relationships between biofilm formation to clonal type, site of isolate collection, and MDR phenotype were evaluated. Furthermore, in patients with relapsing infections, serial strains were assessed for their ability to form biofilms in vitro. Of the 205 clinical isolates tested, 126 strains (61.4%) were observed to form biofilms in vitro at levels greater than or equal to the Staphylococcus epidermidis, positive biofilm producing strain, with P. aeruginosa and S. aureus having the greatest number of biofilm producing strains. Biofilm formation was significantly associated with specific clonal types, the site of isolate collection, and strains positive for biofilm formation were more frequently observed to be MDR. In patients with relapsing infections, the majority of serial isolates recovered from these individuals were observed to be strong biofilm producers in vitro. This study is the first to evaluate biofilm formation in a large collection of infecting clinical isolates representing diverse types of infections. Our results demonstrate: (1) biofilm formation is a heterogeneous property amongst clinical strains which is associated with certain clonal types, (2) biofilm forming strains are more frequently isolated from non-fluid tissues, in particular bone and soft tissues, (3) MDR pathogens are more often biofilm formers, and (4) strains from patients with persistent infections are positive for biofilm formation.", "To assess the incidence, pathogens, and outcome of complicated parapneumonic effusions or empyemas in a medical intensive care unit (MICU) patients with pleural effusions. Prospective study of febrile MICU patients with pleural effusion carried out in a tertiary care hospital between April 2001 and September 2003. The study included 175 patients with a temperature above 38 degrees for more than 8 h with evidence of pleural effusion confirmed by chest radiography and ultrasound. Routine thoracentesis and effusion cultures. The prevalence of complicated parapneumonic effusions or thoracic empyemas in febrile MICU patients with pleural effusions was 45% (78/175). A total of 78 micro-organisms were isolated from the pleural fluid of 58 patients (positive microbiological culture 74%) including aerobic Gram-negative (n=45), aerobic Gram-positive (n=23), anaerobic (n=5), Myobacterium tuberculosis (n=3), and Candida (n=2). The infection-related mortality rate of complicated parapneumonic effusions or empyemic patients in the MICU was 41% (32/78). The development of complicated parapneumonic effusions or thoracic empyemas in MICU patients is a high-mortality disease. The increasing incidence of aerobic Gram-negative pathogens in empyema has become a more urgent problem.", "On the basis of phenotypic analysis, the Klebsiella pneumoniae CG43 derived mutants with deletions of the gene encoding respectively the response regulators KvgA, KvhA, and KvhR were classified into two groups. Group I bacteria carrying either kvgA- or kvhR- exhibited less mucoidy, lower level of capsular polysaccharide (CPS) synthesis and higher LD50 than the parental strain. No apparent change of the group II, including kvhA- and kvhA- kvhR- mutants, was observed. However, the mucoidy of kvhA- kvhR- mutant was found to be diminished after introducing into a kvhA- expressing plasmid. Via promoter-lacZ fusion analysis, kvhA deletion was found to reduce kvhR expression. A regulatory role of KvhA for the expression of kvhR was supported further by EMSA showing a specific binding of KvhA to the putative promoter of kvhR. The promoter activity measurement and EMSA also revealed that KvgA acted as an autoregulator and an activator for the expression of kvhAS and kvhR. In addition, deletion of kvgA suppressed slightly the promoter activity of the cps-orf16-17, and the expression of all three cps transcripts orf1-2, orf3-15, and orf16-17 were reduced in the kvhR- mutant. These suggest that the three homologous response regulators interact to control, in coordination, the bacterial cps expression.", "Endogenous endophthalmitis has been associated with pyogenic hepatic abscess in several recent anecdotal reports. The purpose of this study was to determine the incidence of endophthalmitis associated with pyogenic hepatic abscess, identify the degree of association with Klebsiella pneumoniae as a causative organism, and determine the outcome of treatment. A retrospective study was performed of 352 consecutive patients with a clinical diagnosis of pyogenic hepatic abscess who had been admitted to Chang Gung Memorial Hospital in Kaohsiung between 1986 and 1993. Findings from complete ophthalmologic evaluations and treatment results were recorded. Eleven patients (3.1 percent) with endogenous endophthalmitis (monocular in eight and binocular in three) were found among the 352 cases of pyogenic hepatic abscess. Seven of the patients had diabetes mellitus and their blood glucose was poorly controlled. Only one patient had an intrahepatic stone as the cause of hepatic abscess, the other abscesses were of cryptogenic origin. The causative organism was mainly K. pneumoniae and the diagnosis was made by blood culture in ten patients, hepatic aspirate culture in seven, and vitreous contents culture in three. Systemic antibiotics were given in all patients with endogenous endophthalmitis. Percutaneous catheter drainage for hepatic abscess under echo guidance was performed in seven patients, medical treatment only was performed in three patients, and percutaneous tapping of abscess was done in one patient. All 11 patients were alive at the time of writing. Intravitreous culture followed by injection of antibiotics and steroids was immediately undertaken if septic endophthalmitis was suspected, except in two patients, who lost vision before any treatment was given. In five patients, cefamezin and gentamicin were given, and in four patients vancomycin, amikacin, and dexamethasone were given every three days if necessary. Finally, among the total of 14 eyes, there was blindness in ten, three of these had no light perception initially. In seven patients there had been a delay of treatment longer than one day. In one eye there was \"counting fingers\" vision and in three eyes there remained some vision. Physicians should be alert to the development of endogenous endophthalmitis when a patient with pyogenic hepatic abscess or bacteremia complains of ocular symptoms. Prompt diagnosis and vigorous treatment with intravitreous injections of vancomycin, amikacin, and dexamethasone within 24 hours can save the patient's eyes and vision.", "The high incidence of invasive liver abscess caused by Klebsiella pneumoniae in Taiwan, contrasted with the rareness of this disease in Western countries, has aroused special interest. There have been few detailed reports from other Asian countries. To investigate a current epidemiology of K. pneumoniae liver abscess in Korea and to determine K serotype distribution in K. pneumoniae strains causing liver abscess, we performed a nationwide prospective study. Community-acquired, culture-proven liver abscess cases were enrolled between 2004 and 2005. Etiologies and clinical features were analyzed. K. pneumoniae isolates were serotyped according to K antigen. Meta-analysis was done to determine the time trend of the etiologies of liver abscess in Korea. Out of 371 cases collected prospectively, 290 (78.2%) were caused by K. pneumoniae. Most K. pneumoniae liver abscesses were monomicrobial. Diabetes mellitus was the most common underlying disease (39.9%). Distant metastatic infections were frequently observed (8.7%). magA PCR revealed that 95 (59.4%) out of 160 K. pneumoniae isolates belonged to the K1 serotype. Our study indicates that K. pneumoniae has emerged as a major etiologic agent of liver abscess in Korea, and these emerging infections seem to be attributable to invasive K. pneumoniae strains with capsular K1 serotype.", "The ferric uptake regulator Fur has been reported to repress the expression of rmpA, a regulatory gene for the mucoid phenotype, leading to decreased capsular polysaccharide (CPS) biosynthesis in Klebsiella pneumoniae CG43. Here, quantitative real-time PCR (qRT-PCR) analyses and electrophoretic mobility shift assays showed that Fur also repressed the expression of the CPS regulatory genes rmpA2 and rcsA. Interestingly, deletion of rmpA or rcsA but not rmpA2 from the Δfur strain was able to suppress the deletion effect of Fur. The availability of extracellular iron affected the amount of CPS, suggesting that Fur regulates CPS biosynthesis in an Fe(II)-dependent manner. Increased production of siderophores was observed in the Δfur strain, suggesting that uptake of extracellular iron in K. pneumoniae is regulated by Fur. Fur titration assays and qRT-PCR analyses demonstrated that at least six of the eight putative iron-acquisition systems, identified by a blast search in the contig database of K. pneumoniae CG43, were directly repressed by Fur. We conclude that Fur has a dual role in the regulation of CPS biosynthesis and iron acquisition in K. pneumoniae.", "To investigate the association between Klebsiella pneumoniae-mediated invasive syndrome and underlying diseases in patients and/or K. pneumoniae characteristics, including the rmpA, rmpA2, and magA genes, capsular polysaccharide (cps) K(1) or K(2) serotypes, hypermucoviscosity (HV) phenotype, and extended-spectrum beta-lactamase (ESBL) production. This was a prospective cross-sectional study. The invasive syndrome was detected in 19 of 91 patients (20.9%) with K. pneumoniae infections, and diabetes mellitus was the most common underlying disease (9 of 19). The presence of rmpA or rmpA2 was found in 91.4% of the 35 isolates with the HV phenotype, while in only 17.9% of the 56 isolates without HV phenotype. Multivariate logistic regression analysis showed that the HV phenotype was an independent risk factor for K. pneumoniae-mediated invasive syndrome (odds ratio (OR) 58.24, 95% confidence interval (CI) 7.23-468.87; p < 0.001) and was negatively associated with ESBL production (OR 0.042, 95% CI 0.005-0.331; p=0.003). Binary logistic regression analysis revealed that the invasive syndrome was not influenced by the presence of diabetes mellitus among patients infected with K. pneumoniae positive for the rmpA or rmpA2 gene, HV phenotype, or cps K(1)/K(2) serotype. The HV phenotype of K. pneumoniae contributes to invasive syndrome and is a negative predictor for K. pneumoniae acquisition of ESBLs.", "Bacteremia is a common complication of pneumonia with Klebsiella pneumoniae. In the previous work, we have shown that the lipopolysaccharide (LPS) O-antigen in K. pneumoniae O1:K2 contributes to lethality during pneumonia in part by promoting bacteremia. In the current work, we studied an O-antigen-deficient K. pneumoniae strain to further evaluate this polysaccharide's role in bloodstream infection. Cultured macrophage and murine bacteremia models were studied. In vitro, O-antigen-deficient bacteria, compared with wild-type organisms, were stronger activators of the murine alveolar macrophage cell line MH-S as assessed by nuclear localization of RelA/p65 and by secretion of cytokines and chemokines. O-antigen-deficient Klebsiellae were also more susceptible to killing by murine neutrophils. In vivo, the absence of O-antigen allowed more rapid and complete clearance of bacteria from the bloodstream, liver, and spleen after intravenous injection in mice. Survival was also greater among animals infected with bacteria missing the O-antigen. Gene expression profiling (via reverse transcriptase-polymerase chain reaction of 84 inflammatory mediator complementary DNA) revealed that by 24 h postinfection, the livers and spleens of animals infected with O-antigen-deficient organisms had significantly downregulated cytokine and chemokine expression compared with wild-type infected animals. The O-antigen surface carbohydrate of O1:K2 serotype K. pneumoniae appears to contribute to bacterial virulence by lessening the activation of macrophages, conveying resistance to killing by neutrophils, and by promoting persistent infection in the blood, liver, and spleen after the onset of bacteremia." ]
is protein good for aging?	Higher protein intake is linked to maintenance of muscle mass and strength, but few studies have related protein to physical function and disability in aging.	[ "The progression of the aging process leads to a decreased margin of homeostatic reserve and a reduced ability to accommodate metabolic challenges, including nutritional stress. Nutritional frailty refers to the disability that occurs in old age owing to rapid, unintentional loss of body weight and loss of lean body mass (sarcopenia). Sarcopenia, a loss of muscle mass and strength, contributes to functional impairment. Weight loss is commonly due to a reduction in food intake; its possible etiology includes a host of physiological and nonphysiological causes. The release of cytokines during chronic disease may also be an important determinant of frailty. In addition to being anorectic, cytokines also contribute to lipolysis, muscle protein breakdown, and nitrogen loss. Whereas the multiple causes of nutritional frailty are not completely understood, clinical interventions for weight loss, sarcopenia, and cytokine alterations have been used with modest success.", "An adequate level of protein intake is required to limit the gradual body protein loss observed during ageing. Different factors (cohort age, sex, life conditions) may modify protein intake and distribution. However the precise amounts, as well as their daily distribution which affects protein utilisation and N retention, are unknown in both young and elderly individuals. The hypothesis was tested that protein intake and its distribution over daily meals could be different between the young and elderly. The consumption of six different protein-rich food groups by 292 healthy individuals aged 20-30 and 65-75 years was determined throughout each day for 1 week. The data of the total protein intake and protein intakes at each meal were analysed by ANOVA for each sex separately, using age group as the independent factor. The average protein intake of men was lower in the older age group whilst the opposite trend was seen in women. The distribution of protein intake was different between the two age groups: 56.5 % of the daily protein was eaten at lunch by the elderly but only 47 % (P<0.0001) by the younger subjects. In the elderly subjects, those eating larger amounts consumed a greater proportion of protein-rich foods at dinner than those eating small amounts (30.4 v. 26.2 %, P=0.05). A high level of protein intake was related to a higher meat-product consumption in both the elderly and young individuals. In conclusion, the pattern of protein intake differs significantly between age groups and sexes.", "To preserve muscle mass and therefore limit the risk of disability in older adults protein intake is seen as important factor. Besides the amount of protein, its distribution over the day is thought to affect protein anabolism. This cross-sectional study investigates the association between the amount and distribution of protein intake and frailty in older adults. In 194 community-dwelling seniors (≥75 years) amount of protein intake and its distribution over the day (morning, noon, evening) were assessed using a food frequency questionnaire. Unevenness of protein distribution was calculated as coefficient of variation (CV). Frailty was defined as the presence of at least three, pre-frailty as the presence of one or two of the following criteria: weight loss, exhaustion, low physical activity, low handgrip strength and slow walking speed. 15.4% of the participants were frail, 40.5% were pre-frail. Median (min.-max.) daily protein intake was 77.5 (38.5-131.5) g, 1.07 (0.58-2.27) g/kg body weight (BW) and 15.9 (11.2-21.8) % of energy intake without significant differences between the frailty groups. The risk of frailty did not differ significantly between participants in the higher compared to the lowest quartile of protein intake. Frail participants consumed significantly less protein in the morning (11.9 vs. 14.9 vs. 17.4%, p = 0,007), but more at noon (61.4 vs. 60.8 vs. 55.3%, p = 0.024) than pre-frail and non-frail. The median (min.-max.) CV of protein distribution was highest in frail (0.76 (0.18-1.33)) compared to pre-frail (0.74 (0.07-1.29)) and non-frail (0.68 (0.15-1.24)) subjects (p = 0.024). In this sample of healthy older persons, amount of protein intake was not associated with frailty, but distribution of protein intake was significantly different between frail, pre-frail and non-frail participants. More clinical studies are needed to further clarify the relation between protein intake and frailty.", "Associations between intake of specific nutrients and disease cannot be considered primary effects of diet if they are simply the result of differences between cases and noncases in body size, physical activity, and metabolic efficiency. Epidemiologic studies of diet and disease should therefore be directed at the effect of nutrient intakes independent of total caloric intake in most instances. This is not accomplished with nutrient density measures of dietary intake but can be achieved by employing nutrient intakes adjusted for caloric intake by regression analysis. While pitfalls in the manipulation and interpretation of energy intake data in epidemiologic studies have been emphasized, these considerations also highlight the usefulness of obtaining a measurement of total caloric intake. For instance, if a questionnaire obtained information on only cholesterol intake in a study of coronary heart disease, it is possible that no association with disease would be found even if a real positive effect of a high cholesterol diet existed, since the caloric intake of cases is likely to be less than that of noncases. Such a finding could be appropriately interpreted if an estimate of total caloric intake were available. The relationships between dietary factors and disease are complex. Even with carefully collected measures of intake, consideration of the biologic implications of various analytic approaches is needed to avoid misleading conclusions." ]
The role of monoamines in gastrointestinal neuroimmunomodulation	Recent advances in neurogastroenterology have extended and refined our knowledge on the roles monoamines play in physiology and pathophysiology of the gastrointestinal tract. The catecholamine noradrenaline, as the primary transmitter of postganglionic sympathetic neurons, orchestrates motility and secretory reflexes and controls arterial perfusion as well as immune functions. The catecholamine dopamine is produced by a subpopulation of enteric neurons which possibly use it as transmitter. Serotonin, largely produced by enterochromaffin cells and to a small extent by enteric neurons profoundly affects gut motility, enteric neuron development and is also involved in immunomodulation. However, its mode of action and the relative contribution of non-neuronal versus neuronal serotonin was recently subject to debate again. Histamine, although entirely of non-neuronal origin, is pivotal for gastrointestinal neuroimmunomodulation besides its paracrine effect in gastric HCl production.	[ "1. Ganglion cells of the myenteric plexus of the guinea-pig ileum have been studied with intracellular micro-electrodes.2. Three types of cell were distinguished. Type 1 cells had a high resistance (58 MOmega) and had properties similar to guinea-pig sympathetic ganglion cells. Type 2 cells were also excitable but had a lower resistance (21 MOmega) and showed accommodation to depolarizing current pulses. Type 3 cells were inexcitable.3. Point stimulation within 150 mum excited neurones either antidromically or orthodromically, sometimes both.4. Antidromic responses had a small all-or-nothing component which was subthreshold for the soma spike. Two or more such components sometimes occurred, and were probably due to stimulation of two or more cell processes.5. Excitatory post-synaptic potentials (e.p.s.p.s) were blocked by hexamethonium (400 muM). They progressively declined in amplitude when elicited at frequencies of 0.05 Hz or more, and this is discussed in relation to studies on acetylcholine (ACh) output.6. Many cells often showed a slow after-hyperpolarization following a direct or antidromic spike. Its mechanism and significance are discussed.7. Spontaneous e.p.s.p.s and spikes were occasionally seen.8. Intracellular injection of a fluorescent dye reveals that the neurones have one to seven processes, which usually arise from the poles of the oval soma.", "Serotonin is a major transmitter in the gastrointestinal tract, but little is known about the serotonergic system in the esophagus. The aim of this study was to use multilabel immunofluorescence to characterize serotonin-positive nerve cell bodies and fibers and their relationship with other neuronal and non-neuronal elements in the mouse esophagus. Antibodies against serotonin, vesicular acetylcholine transporter (VAChT), choline acetyltransferase (ChAT), protein gene product 9.5 (PGP 9.5), and α-bungarotoxin (α-BT), were used. Serotonin-containing perikarya represented ∼10% of all PGP 9.5-positive myenteric neurons. Serotonin-positive varicose nerve fibers were found in the lamina muscularis mucosae and present on ∼13% of α-BT-labeled motor endplates in addition to VAChT-immunoreactive motor terminals. As ChAT-positive neurons of the compact formation of the nucleus ambiguus were negative for serotonin, serotonin-positive varicosities on motor endplates are presumed to be of enteric origin. On the other hand, cholinergic ambiguus neurons were densely supplied with serotonin-positive varicosities. The tela submucosa and tunica adventitia contained large numbers of serotonin-positive mast cells, a few of which were in close association with serotonin-positive nerve fibers. The mouse esophagus is endowed with a rich serotonin-positive intrinsic innervation, including enteric co-innervation of striated muscles. Serotonin may modulate vagal motor innervation of esophageal-striated muscles not only at the central level via projections of the raphe nuclei to the nucleus ambiguus but also at the peripheral level via enteric co-innervation. In addition, mast cells represent a non-neuronal source of serotonin, being involved in neuroimmune processes.", "The aim of this investigation was to identify the proportional neurochemical codes of enteric neurons and to determine the specific terminal fields of chemically defined nerve fibers in all parts of the human gastrointestinal (GI) tract. For this purpose, antibodies against the vesicular monoamine transporters (VMAT1/2), the vesicular acetylcholine transporter (VAChT), tyrosine hydroxylase (TH), dopamine beta-hydroxylase (DBH), serotonin (5-HT), vasoactive intestinal peptide (VIP), and protein gene product 9.5 (PGP 9.5) were used. For in situ hybridization (35)S-labeled VMAT1, VMAT2, and VAChT riboprobes were used. In all regions of the human GI tract, 50-70% of the neurons were cholinergic, as judged by staining for VAChT. The human gut unlike the rodent gut exhibits a cholinergic innervation, which is characterized by an extensive overlap with VIPergic innervation. Neurons containing VMAT2 constituted 14-20% of all intrinsic neurons in the upper GI tract, and there was an equal number of TH-positive neurons. In contrast, DBH was absent from intrinsic neurons. Cholinergic and monoaminergic phenotypes proved to be completely distinct phenotypes. In conclusion, the chemical coding of human enteric neurons reveals some similarities with that of other mammalian species, but also significant differences. VIP is a cholinergic cotransmitter in the intrinsic innervation of the human gut. The substantial overlap between VMAT2 and TH in enteric neurons indicates that the intrinsic catecholaminergic innervation is a stable component of the human GI tract throughout life. The absence of DBH from intrinsic catecholaminergic neurons indicates that these neurons have a dopaminergic phenotype.", "The afferent innervation of the gastrointestinal (GI) tract consists of intrinsic and extrinsic sensory neurons that respond to nutrients, chemicals or mechanical stimuli within the gut lumen. Most stimuli do not interact directly with the afferent nerves but instead activate specialised cells in the epithelium in a process of sensory transduction. It is thought that one of the first steps in this process is the release of serotonin (5-HT) from the enterochromaffin (EC) cells. The EC cells are a sub-type of enteroendocrine (EE) cells which are found among the enterocytes of the intestinal epithelium. The EC cells are responsible for the production and storage of the largest pool of 5 HT in the body. Released 5-HT can act on the intrinsic nerves and vagal endings. This review will focus on the role of 5-HT in sensory transduction and examine how the EC cell produces and releases 5-HT. We will explore recent developments that have helped to elucidate some of the proteins that allow EC cells to sense the luminal environment. Finally, we will highlight some of the findings from new studies using electrochemical techniques which allow the real-time recording of 5-HT concentrations near to the EC cell.", "A full description of the terminal architecture of sympathetic axons innervating the gastrointestinal (GI) tract has not been available. To label sympathetic fibers projecting to the gut muscle wall, dextran biotin was injected into the celiac and superior mesenteric ganglia (CSMG) of rats. Nine days postinjection, animals were euthanized and stomachs and small intestines were processed as whole mounts (submucosa and mucosa removed) to examine CSMG efferent terminals. Myenteric neurons were counterstained with Cuprolinic Blue; catecholaminergic axons were stained immunohistochemically for tyrosine hydroxylase. Essentially all dextran-labeled axons (135 of 136 sampled) were tyrosine hydroxylase-positive. Complete postganglionic arbors (n = 154) in the muscle wall were digitized and analyzed morphometrically. Individual sympathetic axons formed complex arbors of varicose neurites within myenteric ganglia/primary plexus and, concomitantly, long rectilinear arrays of neurites within circular muscle/secondary plexus or longitudinal muscle/tertiary plexus. Very few CSMG neurons projected exclusively (i.e., ∼100% of an arbor's varicose branches) to myenteric plexus (∼2%) or smooth muscle (∼14%). With less stringent inclusion criteria (i.e., ≥85% of an axon's varicose branches), larger minorities of neurons projected predominantly to either myenteric plexus (∼13%) or smooth muscle (∼27%). The majority (i.e., ∼60%) of all individual CSMG postganglionics formed mixed, heterotypic arbors that coinnervated extensively (>15% of their varicose branches per target) both myenteric ganglia and smooth muscle. The fact that ∼87% of all sympathetics projected either extensively or even predominantly to smooth muscle, while simultaneously contacting myenteric plexus, is consistent with the view that these neurons control GI muscle directly, if not exclusively. J. Comp. Neurol. 524:2577-2603, 2016. © 2016 Wiley Periodicals, Inc.", "Intraganglionic laminar endings (IGLEs) are special terminal structures of vagal afferent fibers and have been demonstrated in the myenteric plexus of esophagus and stomach. In order to quantitatively map their presence and distribution over the entire gastrointestinal tract, including the small and large intestines, vagal afferents were anterogradely labeled in vivo by microinjections of the fluorescent carbocyanine dye DiI into the left or right nodose ganglion of adult male rats. In the most successfully labeled cases the highest density of IGLEs was found in the stomach, with about half to one-third of the myenteric ganglia receiving at least one IGLE. The proportion of myenteric ganglia innervated by IGLEs decreased in the small intestine; however, because of its large surface area this gut segment was estimated to contain the highest total number of IGLEs. Both the cecum and colon also contained significant numbers of IGLEs. In the stomach, this vagal afferent innervation by IGLEs was more or less lateralized, with less than 20% of labeled IGLEs found on the contralateral side with respect to the injection. The left/ventral vagus contributed a larger proportion of IGLEs to the proximal duodenum, while the right/dorsal vagus contributed a larger proportion of IGLEs to the distal duodenum and jejunum. Laser scanning confocal microscopy on select specimens revealed further structural details. The parent axon typically formed two or more branches that flanked the ganglia laterally, and in turn produced numerous highly arborizing laminar terminal branches that covered one or both flat sides of the ganglion in a dome-like fashion. The similar distribution patterns and structural details suggest a uniform function for the IGLEs throughout the gastrointestinal tract, but there is as yet no clear proof for any of the hypothesized roles as specialized mechanosensors or local effector terminals.", "Pseudouni- or multiaxonal Dogiel type II neurons are the intrinsic primary afferent (sensory) neurons (IPANs) in the guinea pig small intestine. Our aim was to decipher the chemical code of human myenteric type II neurons and to establish their putative vertical projections, i.e., from the myenteric plexus to the submucosa/mucosa. Additionally, we tried to distinguish them chemically from uniaxonal, dendritic type V neurons displaying, at first glance, similar shapes, i.e., smoothly contoured cell bodies with several long processes. Wholemount preparations of the myenteric plexus were immunohistochemically double or triple stained for neurofilaments (NF) and one or two of the following peptides: calbindin, calretinin (CR), calcitonin gene-related peptide (CGRP), somatostatin (SOM) and substance P (SP). In each triple stained wholemount three counts were conducted: (1) NF-positive pseudouni- or multiaxonal (type II) neurons including their reactivities for the above peptides, (2) uniaxonal or NF-negative neurons displaying coreactivities for the above peptides and (3) NF-reactive type V neurons taking into account their reactivities for the above markers. Additionally, type II neurons, which had an axon leading into (disrupted) interconnecting strands towards the submucosa were counted and somal areas of types II and V neurons were measured. The majority of myenteric type II neurons displayed coreactivities for SOM/CR (89.6%), SOM/SP (86.6%) and SP/CR (81.6%), respectively. A minority of type II neurons was positive for CGRP or calbindin. A small population with type III morphology (uniaxonal, long and slender dendrites) displayed the same coreactivities as type II neurons. In contrast, not one single type V neuron was coreactive for SOM/CR, SOM/SP or SP/CR. Out of 627 type II neurons counted in six wholemounts, 84 type II neurons displayed an axon which could be followed into disrupted interconnecting strands indicating a vertical projection pattern. Somal areas of type II neurons were twice as big as those of type V neurons (904+/-210 versus 449+/-110 microm(2)). In conclusion, most human myenteric type II neurons contain SOM, SP and CR. We suggest they are the human IPANs. Type V neurons are both morphologically and chemically distinctly different from type II neurons and may represent descending interneurons. Further studies have to decipher the type-specific chemical code of type II neurons distinguishing them also from type III neurons.", "In dog ileum, axons containing immunoreactivity for tyrosine hydroxylase (TH) and for DOPA decarboxylase (DDC) invest the neurones of the enteric ganglia and are present around arterioles, in the deep plexus of the circular muscle and in the laminar propria of the mucosal villi. Immunoreactivity for serotonin (5-HT) was present in mucosal enterochromaffin cells and in varicose axons investing cells of the submucous plexus, but not in axons in myenteric plexus, circular muscle or mucosa. No enteric neuronal cell bodies were immunoreactive for DDC or for 5-HT. Two weeks after extrinsic denervation of the ileum, all TH staining was absent. By contrast, the pattern of DDC staining was unchanged, except around blood vessels. We conclude that motility of dog ileum is likely to be regulated by sympathetic noradrenergic inputs and by intrinsic serotonergic and 'amine-handling' neurones. Dopaminergic innervation of dog ileum appears to be restricted to a sparse vasomotor supply.", "The tertiary component of the myenteric plexus consists of interlacing fine nerve fibre bundles that run between its principal ganglia and connecting nerve strands. It was revealed by zinc iodide-osmium impregnation and substance P immunohistochemistry at the light-microscope level. The plexus was situated against the inner face of the longitudinal muscle and was present along the length of the small intestine at a density that did not vary markedly from proximal to distal. Nerve bundles did not appear to be present in the longitudinal muscle as judged by light microscopy, although numerous fibre bundles were encountered within the circular muscle layer. At the ultrastructural level, nerve fibre bundles of the tertiary plexus were found in grooves formed by the innermost layer of longitudinal smooth muscle cells. In the distal parts of the small intestine, some of these nerve fibre bundles occasionally penetrated the longitudinal muscle coat. Vesiculated profiles in nerve fibre bundles of the tertiary plexus contained variable proportions of small clear and large granular vesicles; they often approached to within 50-200 nm of the longitudinal smooth muscle cells. Fibroblast-like cells lay between strands of the tertiary plexus and the circular muscle but were never intercalated between nerve fibre varicosities and the longitudinal muscle. These anatomical relationships are consistent with the tertiary plexus being the major site of neurotransmission to the longitudinal muscle of the guinea-pig small intestine.", "Biotinylated dextran amines (BDA) are highly sensitive tools for anterograde and retrograde pathway tracing studies of the nervous system. BDA can be reliably delivered into the nervous system by iontophoretic or pressure injection and visualized with an avidin-biotinylated HRP (ABC) procedure, followed by a standard or metal-enhanced diaminobenzidine (DAB) reaction. High molecular weight BDA (10 k) yields sensitive and exquisitely detailed labeling of axons and terminals, while low molecular weight BDA (3 k) yields sensitive and detailed retrograde labeling of neuronal cell bodies. The detail of neuronal cell body labeling can be Golgi-like. BDA tolerates EM fixation and processing well and can, therefore, be readily used in ultrastructural studies. Additionally, BDA can be combined with other anterograde or retrograde tracers (e.g. PHA-L or cholera toxin B fragment) and visualized either by multi-color DAB multiple-labeling - if permanent labels are desired, or by using multiple simultaneous immunofluorescence - if fluorescence viewing is desired. In the same manner, BDA pathway tracing and neurotransmitter immunolabeling can be combined. Note that BDA pathway tracing can also be combined with anterograde or retrograde labeling with fluorescent dextran amines, if one wishes to exclusively use tracers with the favorable transport properties and sensitivities of dextran amines. In this case, the BDA can be visualized together with the fluorescent dextran amines using fluorescence labeling for the BDA, or the fluorescent dextran amines can be visualized together with the BDA by multicolor DAB labeling via immunolabeling of the fluorescent dextran amines using anti-fluorophore antisera. BDA is, thus, a flexible and valuable pathway tracing tool that has gained widespread popularity in recent years." ]
How can the Internet help end and not fuel the opioid public health emergency?	The United States is in the midst of an opioid public health emergency, one that is also influenced by a convergence of Internet-based technology, health policy, and the need for stakeholder collaboration and action around the need to combat the illicit online sales of opioids by illegal online pharmacies and digital drug dealers. This risk is not new, however, with calls to actively reduce online opioid availability as online pharmacies use a growing array of digital channels, including search engines, social media platforms, and the dark Web. In response, the US Food and Drug Administration convened a special June 2018 summit bringing together technology companies, government agencies, researchers, and advocacy groups with the goal of collaboratively developing and implementing solutions to tackle the problem. Yet after this meeting, stakeholders remain fragmented in approaches despite the availability of technology that can detect, classify, and report illicit sellers who are in direct violation of Federal law. Despite ongoing challenges, advances in data science and the resources and expertise technology companies can contribute will be a key factor in ensuring that the Internet helps end and not fuel the public health emergency of opioid abuse.	[ "On December 6 and 7, 2017, the US Department of Health and Human Services (HHS) hosted its first Code-a-Thon event aimed at leveraging technology and data-driven solutions to help combat the opioid epidemic. The authors—an interdisciplinary team from academia, the private sector, and the US Centers for Disease Control and Prevention—participated in the Code-a-Thon as part of the prevention track. The aim of this study was to develop and deploy a methodology using machine learning to accurately detect the marketing and sale of opioids by illicit online sellers via Twitter as part of participation at the HHS Opioid Code-a-Thon event. Tweets were collected from the Twitter public application programming interface stream filtered for common prescription opioid keywords in conjunction with participation in the Code-a-Thon from November 15, 2017 to December 5, 2017. An unsupervised machine learning–based approach was developed and used during the Code-a-Thon competition (24 hours) to obtain a summary of the content of the tweets to isolate those clusters associated with illegal online marketing and sale using a biterm topic model (BTM). After isolating relevant tweets, hyperlinks associated with these tweets were reviewed to assess the characteristics of illegal online sellers. We collected and analyzed 213,041 tweets over the course of the Code-a-Thon containing keywords codeine, percocet, vicodin, oxycontin, oxycodone, fentanyl, and hydrocodone. Using BTM, 0.32% (692/213,041) tweets were identified as being associated with illegal online marketing and sale of prescription opioids. After removing duplicates and dead links, we identified 34 unique “live” tweets, with 44% (15/34) directing consumers to illicit online pharmacies, 32% (11/34) linked to individual drug sellers, and 21% (7/34) used by marketing affiliates. In addition to offering the “no prescription” sale of opioids, many of these vendors also sold other controlled substances and illicit drugs. The results of this study are in line with prior studies that have identified social media platforms, including Twitter, as a potential conduit for supply and sale of illicit opioids. To translate these results into action, authors also developed a prototype wireframe for the purposes of detecting, classifying, and reporting illicit online pharmacy tweets selling controlled substances illegally to the US Food and Drug Administration and the US Drug Enforcement Agency. Further development of solutions based on these methods has the potential to proactively alert regulators and law enforcement agencies of illegal opioid sales, while also making the online environment safer for the public.", "Online pharmacies are companies that sell pharmaceutical preparations, including prescription-only drugs, on the Internet. Very little is known about this phenomenon because many online pharmacies operate from remote countries, where legal bases and business practices are largely inaccessible to international research. The aim of the study was to perform an up-to-date and comprehensive review of the scientific literature focusing on the broader picture of online pharmacies by scanning several scientific and institutional databases, with no publication time limits. We searched 4 electronic databases up to January 2011 and the gray literature on the Internet using the Google search engine and its tool Google Scholar. We also investigated the official websites of institutional agencies (World Health Organization, and US and European centers for disease control and drug regulation authorities). We focused specifically on online pharmacies offering prescription-only drugs. We decided to analyze and report only articles with original data, in order to review all the available data regarding online pharmacies and their usage. We selected 193 relevant articles: 76 articles with original data, and 117 articles without original data (editorials, regulation articles, or the like) including 5 reviews. The articles with original data cover samples of online pharmacies in 47 cases, online drug purchases in 13, consumer characteristics in 15, and case reports on adverse effects of online drugs in 12. The studies show that random samples with no specific limits to prescription requirements found that at least some websites sold drugs without a prescription and that an online questionnaire was a frequent tool to replace prescription. Data about geographical characteristics show that this information can be concealed in many websites. The analysis of drug offer showed that online a consumer can get virtually everything. Regarding quality of drugs, researchers very often found inappropriate packaging and labeling, whereas the chemical composition usually was not as expected in a minority of the studies' samples. Regarding consumers, the majority of studies found that not more than 6% of the samples had bought drugs online. Online pharmacies are an important phenomenon that is continuing to spread, despite partial regulation, due to intrinsic difficulties linked to the impalpable and evanescent nature of the Web and its global dimension. To enhance the benefits and minimize the risks of online pharmacies, a 2-level approach could be adopted. The first level should focus on policy, with laws regulating the phenomenon at an international level. The second level needs to focus on the individual. This approach should aim to increase health literacy, required for making appropriate health choices, recognizing risks and making the most of the multitude of opportunities offered by the world of medicine 2.0.", "With the rapid development of new psychoactive substances (NPS) and changes in the use of more traditional drugs, it is increasingly difficult for researchers and public health practitioners to keep up with emerging drugs and drug terms. Substance use surveys and diagnostic tools need to be able to ask about substances using the terms that drug users themselves are likely to be using. Analyses of social media may offer new ways for researchers to uncover and track changes in drug terms in near real time. This study describes the initial results from an innovative collaboration between substance use epidemiologists and linguistic scientists employing techniques from the field of natural language processing to examine drug-related terms in a sample of tweets from the United States. The objective of this study was to assess the feasibility of using distributed word-vector embeddings trained on social media data to uncover previously unknown (to researchers) drug terms. In this pilot study, we trained a continuous bag of words (CBOW) model of distributed word-vector embeddings on a Twitter dataset collected during July 2016 (roughly 884.2 million tokens). We queried the trained word embeddings for terms with high cosine similarity (a proxy for semantic relatedness) to well-known slang terms for marijuana to produce a list of candidate terms likely to function as slang terms for this substance. This candidate list was then compared with an expert-generated list of marijuana terms to assess the accuracy and efficacy of using word-vector embeddings to search for novel drug terminology. The method described here produced a list of 200 candidate terms for the target substance (marijuana). Of these 200 candidates, 115 were determined to in fact relate to marijuana (65 terms for the substance itself, 50 terms related to paraphernalia). This included 30 terms which were used to refer to the target substance in the corpus yet did not appear on the expert-generated list and were therefore considered to be successful cases of uncovering novel drug terminology. Several of these novel terms appear to have been introduced as recently as 1 or 2 months before the corpus time slice used to train the word embeddings. Though the precision of the method described here is low enough as to still necessitate human review of any candidate term lists generated in such a manner, the fact that this process was able to detect 30 novel terms for the target substance based only on one month's worth of Twitter data is highly promising. We see this pilot study as an important proof of concept and a first step toward producing a fully automated drug term discovery system capable of tracking emerging NPS terms in real time.", "Permanently recalled drugs are a public health concern if they remain accessible in violation of applicable regulation. Illicit online pharmacies act as an alternative form of access and have been associated with the sale to patients of counterfeit/falsified/fraudulent/substandard drugs. We wished to determine if permanently recalled and significantly restricted drugs were illegally marketed for sale online. The study was conducted in two phases with two objectives. The first phase attempted to identify drugs subject to permanent recall in certain major pharmaceutical markets as well as those listed as recalled or significantly restricted by the United Nations. We also examined the market authorization status of identified drugs in China and India. The second phase used structured searches on the Internet to determine if identified drugs were marketed for sale online. The World Wide Web. After identification of permanently recalled and restricted drugs we conducted Internet searches for illegal \"no prescription\" marketing events. We assessed the form of marketing, whether a site offered direct-to-patient sale, use of social media marketing, and the site's compliance status with external monitoring bodies. Number of recalled drugs marketed as available for purchase on the Internet. We identified 16 class I equivalent permanently recalled or restricted drugs, 56.3 % (n = 9) of which maintained market authorization in either China or India. Half (n = 8) were marketed for sale online without a prescription direct-to-patient. Use of social media marketing was mixed, with only 18.8 % (n = 3) of recalled drugs having a presence on Facebook, though 50.0 % (n = 8) had content on Twitter. We also found the majority (68.8 %, n = 11) were available and marketed for sale by vendors on the wholesale/business-to-business website alibaba.com primarily as active pharmaceutical ingredient. Despite efforts in several countries to restrict access to these drugs or permanently remove them from the market, our study indicates that various sources actively market recalled drugs for sale online. Drug regulators, public health agencies, and law enforcement officials should act with urgency to appropriately restrict and regulate these sales to protect global patients and consumers." ]
[Pathogenesis and treatment of periodontal and peri-implantitis].	Despite many discoveries over the past 20 years regarding the etio-pathogenesis of periodontal and peri-implant diseases, as well as significant advances in our understanding of microbial biofilms, the incidence of these pathologies still continues to rise. This review presents a general overview of the main protagonists and phenomena involved in oral health and disease. A special emphasis on the role of certain keystone pathogens in periodontitis and peri-implantitis is underlined. Their capacity to bring a dysregulation of the homeostasis with their host and the microbial biofilm lifestyle are also discussed. Finally, the current treatment principles of periodontitis and peri-implantitis are presented and their limits exposed. This leads to realize that new strategies must be developed and studied to overcome the shortcomings of existing approaches.	[ "Porphyromonas gingivalis, a periodontal pathogen, can invade primary cultures of gingival epithelial cells. Optimal invasion occurred at a relatively low multiplicity of infection (i.e., 100) and demonstrated saturation at a higher multiplicity of infection. Following the lag phase, during which bacteria invaded poorly, invasion was independent of growth phase. P. gingivalis was capable of replicating within the epithelial cells. Invasion was an active process requiring both bacterial and epithelial cell energy production. Invasion was sensitive to inhibitors of microfilaments and microtubules, demonstrating that epithelial cell cytoskeletal rearrangements are involved in bacterial entry. P. gingivalis, but not epithelial cell, protein synthesis was necessary for invasion. Invasion within the epithelial cells was not blocked by inhibitors of protein kinase activity. Invasion was inhibited by protease inhibitors, suggesting that P. gingivalis proteases may be involved in the invasion process. Low-passage clinical isolates of P. gingivalis invaded with higher efficiency than the type strain. Serum inhibited invasion of the type strain but had no effect on the invasion of a clinical isolate. Invasion of gingival epithelial cells by P. gingivalis may contribute to the pathology of periodontal diseases.", "Peri-implantitis has gained significant clinical attention in recent years. This disease is an inflammatory reaction to microorganisms around dental implants. Due to the limited accessibility, non-invasive antimicrobial strategies are of high interest. An unexpected approach to implant disinfection may evolve from electrolysis. Given the electrical conductivity of titanium implants, alkalinity or active oxidants can be generated in body fluids. We investigated the use of dental titanium implants as electrodes for the local generation of disinfectants. Our hypothesis was that electrolysis can reduce viable counts of adhering bacteria, and that this reduction should be greater if active oxidative species are generated. As model systems, dental implants, covered with a mono-species biofilm of Escherichia coli C43, were placed in photographic gelatin prepared with physiological saline. Implants were treated by a continuous current of 0-10 mA for 15 minutes. The reduction of viable counts was investigated on cathodes and anodes. In separate experiments, the local change in pH was visualized using color indicators embedded in the gelatin. Oxidative species were qualitatively detected by potassium iodide-starch paper. The in situ generated alkaline environment around cathodic implants caused a reduction of up to 2 orders of magnitude in viable E. coli counts. On anodic implants, in contrast to cathodic counterparts, oxidative species were detected. Here, a current of merely 7.5 mA caused complete kill of the bacteria. This laboratory study shows that electrochemical treatment may provide access to a new way to decontaminate dental implants in situ.", "Small samples of hydroxyapatite (HA) beads were coated with 10 microL of either saliva, serum, human crevicular fluid, or a preparation of lysosomal enzymes from human polymorphonuclear leucocytes (PMN), before being added to suspensions of Treponema denticola. The beads were then observed with the scanning electron microscope. Abundant T. denticola were found to adhere to HA or HA coated with saliva, serum, or crevicular fluid. Coating the beads with lysosomal enzymes consistently prevented the adhesion of T. denticola. Adhesion of treponemes to hard surfaces, modulated by enzymes from PMNs, could represent a new virulence factor for these bacteria.", "The expression of adhesion molecules and the local production of chemotactic cytokines within the epithelium are considered to be key events in neutrophil (PMN) migration at sites of mucosal infections. In their journey toward the gingival sulcus, PMNs have been shown to selectively migrate through the junctional epithelium. Little, however, is known about the molecular mechanisms involved in this key process aimed at the control of subgingival bacterial plaque. This investigation describes the expression of IL-8 mRNA-positive cells and the establishment of a gradient of intercellular adhesion molecule-1 (ICAM-1) receptors within the junctional epithelium of clinically healthy gingiva. Expression of ICAM-1 and IL-8 was topographically associated with the area of PMN migration; i.e., the junctional epithelium. Levels of ICAM-1 expression increased from the basal cells toward the surface of the junctional epithelium and thus toward areas exposed to bacterial challenges. IL-8 mRNA-positive cells were also present at highest density in the most superficial junctional epithelial layers. The combination of the haptotactic stimuli, resulting from the interaction of the PMN's beta2 integrin receptors with the gradient of ICAM-1 expression, and the location of IL-8 mRNA-positive cells, consistent with the establishment of a discrete PMN chemotactic source, may play an important physiologic role in efficiently routing PMNs to the gingival sulcus. This process contributes to the maintenance of a local host-parasite equilibrium and to the limitation of PMN-associated tissue damage.", "The Global Burden of Disease (GBD) 2010 Study produced comparable estimates of the burden of 291 diseases and injuries in 1990, 2005, and 2010. This article reports on the global burden of untreated caries, severe periodontitis, and severe tooth loss in 2010 and compares those figures with new estimates for 1990. We used disability-adjusted life-years (DALYs) and years lived with disability (YLDs) metrics to quantify burden. Oral conditions affected 3.9 billion people, and untreated caries in permanent teeth was the most prevalent condition evaluated for the entire GBD 2010 Study (global prevalence of 35% for all ages combined). Oral conditions combined accounted for 15 million DALYs globally (1.9% of all YLDs; 0.6% of all DALYs), implying an average health loss of 224 years per 100,000 population. DALYs due to oral conditions increased 20.8% between 1990 and 2010, mainly due to population growth and aging. While DALYs due to severe periodontitis and untreated caries increased, those due to severe tooth loss decreased. DALYs differed by age groups and regions, but not by genders. The findings highlight the challenge in responding to the diversity of urgent oral health needs worldwide, particularly in developing communities.", "In order to further characterize cellular invasion by enteropathogenic Escherichia coli (EPEC), we compared invasion of HEp-2 cells by EPEC and enteroinvasive E. coli (EIEC). We used a gentamicin HEp-2 cell assay and measured bacterial recovery under conditions of varying incubation time and temperature, and in the presence or absence of inhibitors of cellular microfilaments and microtubules. We found that, unlike EIEC, EPEC did not rapidly multiply within HEp-2 cell but invaded well at 32 degrees C. While microfilament inhibitors reduced invasion by both EIEC and EPEC, microtubule inhibitors reduced invasion by EPEC only. These results suggest that EPEC and EIEC differ in their mechanisms of epithelial cell invasion.", "Since biofilms show strong resistance to conventional disinfectants and antimicrobials, control of initial bacterial adhesion is generally accepted as one of the most effective strategies for preventing biofilm formation. Although electrical methods have been widely studied, the specific properties of cathodic, anodic, and block currents that influence the bacterial detachment and inactivation remained largely unclear. This study investigated the specific role of electric currents in the detachment and inactivation of bacteria adhered to an electrode surface. A real-time bacterial adhesion observation and control system was employed that consisted of Pseudomonas aeruginosa PAO1 (PAO1) with green fluorescent protein as the indicator microorganism and a flow cell reactor mounted on a fluorescent microscope. The results suggest that the bacteria that remained on the electrode surface after application of a cathodic current were alive, although the extent of detachment was significant. In contrast, when an anodic current was applied, the bacteria that remained on the surface became inactive with time, although bacterial detachment was not significant. Further, under these conditions, active bacterial motions were observed, which weakened the binding between the electrode surface and bacteria. This phenomenon of bacterial motion on the surface can be used to maximize bacterial detachment by manipulation of the shear rate. These findings specific for each application of a cathodic or anodic electric current could successfully explain the effectiveness of block current application in controlling bacterial adhesion." ]
The effect of type XI collagen on cell behaviour and mechanical performance in a zebrafish mutant	Collagen is the major structural component of cartilage, and mutations in the genes encoding type XI collagen are associated with severe skeletal dysplasias (fibrochondrogenesis and Stickler syndrome) and early-onset osteoarthritis (OA). The impact of the lack of type XI collagen on cell behaviour and mechanical performance during skeleton development is unknown. We studied a zebrafish mutant for	[ "In order for functional and sport specific activities to occur, knee flexion and extension range of motion (ROM) is necessary. Loss of full ROM at the knee joint can be detrimental to the function of the lower extremity and treatment is needed to regain full function of ROM. Research supports the use of the sustained force to increase knee ROM. This article presents a unique method of attaining sustained force. The technique is cost effective, involves equipment already available in most physical therapy clinics, conserves time, and provides consistent force overtime without causing the therapist fatigue. Despite the fact clinical research has been performed, a poor appreciation exists for the appropriate clinical use of sports massage. Additional studies examining the physiological and psychological effects of sports massage are necessary in order to assist the sports physical therapist in developing and implementing clinically significant evidence based programs or treatments.", "Stickler syndrome is caused by mutations in genes encoding type II and type XI collagens. About 85% of the pathogenic variants is found in COL2A1 (Stickler type 1), whereas a minority of mutations has been reported in COL11A1 (Stickler type 2) and COL11A2 (Stickler type 3). Beside the typical skeletal and orofacial manifestations, ocular anomalies are predominantly present in type 1 and type 2, while hearing loss is more pronounced in type 2 and type 3. We performed COL11A1 mutation analysis for 40 type 2 Stickler patients and COL11A2 mutation analysis for five type 3 Stickler patients, previously all COL2A1 mutation-negative, using targeted next-generation sequencing (NGS) whereas whole-exome sequencing (WES) was performed in parallel for two patients. Three patients were analyzed for both genes due to unclear ocular findings. In total 14 COL11A1 and two COL11A2 mutations could be identified, seven of which are novel. Splice site alterations are the most frequent mutation type, followed by glycine substitutions. In addition, six variants of unknown significance (VUS) have been found. Identical mutations and variants were identified with both NGS techniques. We expand the mutation spectrum of COL11A1 and COL11A2 in Stickler syndrome patients and show that targeted NGS is an efficient and cost-effective molecular tool in the genetic diagnosis of Stickler syndrome, whereas the more standardized WES might be an alternative approach.", "Increasing evidence points to a strong genetic component to osteoarthritis (OA) and that certain changes that occur in osteoarthritic cartilage recapitulate the developmental process of endochondral ossification. As zebrafish are a well validated model for genetic studies and developmental biology, our objective was to establish the spatiotemporal expression pattern of a number of OA susceptibility genes in the larval zebrafish providing a platform for functional studies into the role of these genes in OA. We identified the zebrafish homologues for Mcf2l, Gdf5, PthrP/Pthlh, Col9a2, and Col10a1 from the Ensembl genome browser. Labelled probes were generated for these genes and in situ hybridisations were performed on wild type zebrafish larvae. In addition, we generated transgenic reporter lines by modification of bacterial artificial chromosomes (BACs) containing full length promoters for col2a1 and col10a1. For the first time, we show the spatiotemporal expression pattern of Mcf2l. Furthermore, we show that all six putative OA genes are dynamically expressed during zebrafish larval development, and that all are expressed in the developing skeletal system. Furthermore, we demonstrate that the transgenic reporters we have generated for col2a1 and col10a1 can be used to visualise chondrocyte hypertrophy in vivo. In this study we describe the expression pattern of six OA susceptibility genes in zebrafish larvae and the generation of two new transgenic lines marking chondrocytes at different stages of maturation. Moreover, the tools used demonstrate the utility of the zebrafish model for functional studies on genes identified as playing a role in OA.", "Two missense polymorphisms of WNT16 were associated with hip bone mineral density (BMD), the buckling ratio of the femoral neck, calcaneal ultrasound and hip fractures in individuals under 80 years of age. These results confirm the association of the WNT16 gene with bone mass and osteoporotic fractures. Osteoporosis has a strong genetic component. Wnt ligands stimulate the differentiation of osteoblast precursors and play a major role in skeletal homeostasis. Therefore, the aim of this study was to explore the association of allelic variants of the WNT16 gene with BMD, other structural parameters of bone and osteoporotic hip fractures. Six single nucleotide polymorphisms were analysed in 1,083 Caucasian individuals over 49 years of age. Two missense polymorphisms (rs2908004 and rs2707466) were associated with femoral neck BMD, with average differences across genotypes of 35 mg/cm(2) (p = 0.00037 and 0.0015, respectively). Likewise, the polymorphisms were associated with calcaneal quantitative ultrasound parameters (p = 0.00004 and 0.0014, respectively) and the buckling ratio, an index of cortical instability of the femoral neck (p = 0.0007 and 0.0029, respectively). Although there were no significant differences in the genotype frequency distributions between 294 patients with hip fractures and 670 controls, among the subgroup under 80 years of age, TT genotypes were underrepresented in patients with fractures (odds ratio 0.50; CI 0.27-0.94). Common missense polymorphisms of the WNT16 gene are associated with BMD at the hip, calcaneal ultrasound and the buckling ratio of the femoral neck, as well as with hip fractures in individuals under 80 years of age. Overall, these results confirm the association of the WNT16 locus with BMD identified in genome-wide association studies and support its role in determining the risk of osteoporotic fractures.", "The zebrafish embryo develops a series of anatomically distinct slow twitch muscle fibres that characteristically express genes encoding lineage-specific isoforms of sarcomeric proteins such as MyHC and troponin. We show here that different subsets of these slow fibres express distinct members of a tandem array of slow MyHC genes. The first slow twitch muscle fibres to differentiate, which are specified by the activity of the transcription factor Prdm1 (also called Ubo or Blimp1) in response to Hedgehog (Hh) signalling, express the smyhc1 gene. Subsequently, secondary slow twitch fibres differentiate in most cases independently of Hh activity. We find that although some of these later-forming fibres also express smyhc1, others express smyhc2 or smyhc3. We show that the smyhc1-positive fibres express the ubo (prdm1) gene and adopt fast twitch fibre characteristics in the absence of Prdm1 activity, whereas those that do not express smyhc1 can differentiate independently of Prdm1 function. Conversely, some smyhc2-expressing fibres, although independent of Prdm1 function, require Hh activity to form. The adult trunk slow fibres express smyhc2 and smyhc3, but lack smyhc1 expression. The different slow fibres in the craniofacial muscles variously express smyhc1, smyhc2 and smyhc3, and all differentiate independently of Prdm1.", "Osteoarthritis (OA) has traditionally been classified as a noninflammatory arthritis; however, the dichotomy between inflammatory and degenerative arthritis is becoming less clear with the recognition of a plethora of ongoing immune processes within the OA joint and synovium. Synovitis is defined as inflammation of the synovial membrane and is characteristic of classical inflammatory arthritidies. Increasingly recognized is the presence of synovitis in a significant proportion of patients with primary OA, and based on this observation, further studies have gone on to implicate joint inflammation and synovitis in the pathogenesis of OA. However, clinical OA is not one disease but a final common pathway secondary to many predisposing factors, most notably age, joint trauma, altered biomechanics, and obesity. How such biochemical and mechanical processes contribute to the progressive joint failure characteristic of OA is tightly linked to the interplay of joint damage, the immune response to perceived damage, and the subsequent state of chronic inflammation resulting in propagation and progression toward the phenotype recognized as clinical OA. This review will discuss a wide range of evolving data leading to our current hypotheses regarding the role of immune activation and inflammation in OA onset and progression. Although OA can affect any joint, most commonly the knee, hip, spine, and hands, this review will focus primarily on OA of the knee as this is the joint most well characterized by epidemiologic, imaging, and translational studies investigating the association of inflammation with OA.", "The primary goal of this body of work is to suggest a standardized system for histopathological assessment of experimental surgical instability models of osteoarthritis (OA) in rabbits, building on past experience, to achieve comparability of studies from different centres. An additional objective is to review methodologies that have been employed in the past for assessing OA in rabbits with particular reference to the surgical anterior cruciate ligament transection (ACLT) model. A panel of scientists and clinician-scientists with recognized expertise in assessing rabbit models of OA reviewed the literature to provide a critical appraisal of the methods that have been employed to assess both macroscopic and microscopic changes occurring in rabbit joint tissues in experimental OA. In addition, a validation of the proposed histologic histochemical grading system was performed. The ACLT variant of the surgical instability model in skeletally mature rabbits is the variation most capable of reproducing the entire range of cartilage, synovial and bone lesions recognized to be associated with OA. These lesions can be semiquantitatively graded using macroscopic and microscopic techniques. Further, as well as cartilage lesions, this ACLT model can produce synovial and bone lesions similar to that of human OA. The ACLT variant of the surgical instability model in rabbits is a reproducible and effective model of OA. The cartilage lesions in this model and their response to therapy can be graded according to an adapted histological and histochemical grading system, though also this system is to some extent subjective and, thus, neither objective nor entirely reproducible." ]
Reaction time variability and social functioning in children at risk for ADHD	Reaction time variability (RTV) is a ubiquitous phenomenon in Attention-Deficit/Hyperactivity Disorder (ADHD). Few studies have examined RTV in relation to functional outcomes such as social impairment in children with ADHD. In this exploratory study, we investigated whether RTV is associated with social functioning in children at risk for ADHD. Specifically, we explored the association between RTV (tau derived from correct go trials of a Stop-Signal task) and social functioning in 198 children ages 7-12 years referred for an ADHD evaluation. Social functioning measures included child and/or parent ratings of social competence, aggression, social problems, and impairment in relationships. In regression analyses that also included Oppositional Defiant Disorder symptoms and sex, higher RTV was significantly associated with lower ratings of social competence, and higher proactive/reactive aggression ratings on the child self-report measures. RTV was not significantly associated with parent report of social functioning or relationship impairment. This study provides preliminary evidence that RTV may be associated with social functioning in children at risk for ADHD. We propose that lapses of attention affecting cognitive control may also negatively impact social information processing thereby affecting social functioning. Replication is warranted and longitudinal studies are needed to investigate whether RTV predicts social dysfunction in ADHD.	[ "Literature on the contributions of social cognitive and emotion processes to children's social competence is reviewed and interpreted in the context of an integrated model of emotion processes and cognition in social information processing. Neurophysiological and functional evidence for the centrality of emotion processes in personal-social decision making is reviewed. Crick and Dodge's model is presented as a cognitive model of social decision making, and a revised model is proposed into which emotion processes are integrated. Hypotheses derived from the proposed model are described.", "Children with ADHD demonstrate increased frequent \"lapses\" in performance on tasks in which the stimulus presentation rate is externally controlled, leading to increased variability in response times. It is less clear whether these lapses are also evident during performance on self-paced tasks, e.g., rapid automatized naming (RAN), or whether RAN inter-item pause time variability uniquely predicts reading performance. A total of 80 children aged 9 to 14 years-45 children with attention-deficit/hyperactivity disorder (ADHD) and 35 typically developing (TD) children-completed RAN and reading fluency measures. RAN responses were digitally recorded for analyses. Inter-stimulus pause time distributions (excluding between-row pauses) were analyzed using traditional (mean, standard deviation [SD], coefficient of variation [CV]) and ex-Gaussian (mu, sigma, tau) methods. Children with ADHD were found to be significantly slower than TD children (p < .05) on RAN letter naming mean response time as well as on oral and silent reading fluency. RAN response time distributions were also significantly more variable (SD, tau) in children with ADHD. Hierarchical regression revealed that the exponential component (tau) of the letter-naming response time distribution uniquely predicted reading fluency in children with ADHD (p < .001, ΔR2 = .16), even after controlling for IQ, basic reading, ADHD symptom severity and age. The findings suggest that children with ADHD (without word-level reading difficulties) manifest slowed performance on tasks of reading fluency; however, this \"slowing\" may be due in part to lapses from ongoing performance that can be assessed directly using ex-Gaussian methods that capture excessively long response times.", "Fluent reading depends on a complex set of cognitive processes that must work together in perfect concert. Rapid automatized naming (RAN) tasks provide insight into this system, acting as a microcosm of the processes involved in reading. In this review, we examine both RAN and reading fluency and how each has shaped our understanding of reading disabilities. We explore the research that led to our current understanding of the relationships between RAN and reading and what makes RAN unique as a cognitive measure. We explore how the automaticity that supports RAN affects reading across development, reading abilities, and languages, and the biological bases of these processes. Finally, we bring these converging areas of knowledge together by examining what the collective studies of RAN and reading fluency contribute to our goals of creating optimal assessments and interventions that help every child become a fluent, comprehending reader.", "Children with attention-deficit/hyperactivity disorder (ADHD) often encounter problems in social interactions with peers and are confronted with peer rejection and social isolation. The most common approach to social problems in children is social skills training. This intervention concept represents a variable mixture of cognitive-behavioral intervention elements. In this article the outcome of social skills training (SST) for children with ADHD is reviewed. Four experimental SSTs are detected and analyzed for potential mediators and moderators of treatment efficacy. Candidate mediators (social cognitive skills, parenting style and medication-induced reduction of key symptoms) are discussed within an empirical and theoretical context. Candidate moderators (subtype, comorbidity, gender and age) are evaluated for their empirical support. It is argued that, although fragmented, there is ample evidence and knowledge to adapt the SST-paradigm towards the specific needs of children suffering from ADHD and to guide future research towards more effective, \"well established\" interventions.", "Attention deficit disorder (ADHD) is commonly associated with inhibitory dysfunction contributing to typical behavioral symptoms like impulsivity or hyperactivity. However, some studies analyzing intraindividual variability (IIV) of reaction times in children with ADHD (cADHD) question a predominance of inhibitory deficits. IIV is a measure of the stability of information processing and provides evidence that longer reaction times (RT) in inhibitory tasks in cADHD are due to only a few prolonged responses which may indicate deficits in sustained attention rather than inhibitory dysfunction. We wanted to find out, whether a slowing in inhibitory functioning in adults with ADHD (aADHD) is due to isolated slow responses. Computing classical RT measures (mean RT, SD), ex-Gaussian parameters of IIV (which allow a better separation of reaction time (mu), variability (sigma) and abnormally slow responses (tau) than classical measures) as well as errors of omission and commission, we examined response inhibition in a well-established GoNogo task in a sample of aADHD subjects without medication and healthy controls matched for age, gender and education. We did not find higher numbers of commission errors in aADHD, while the number of omissions was significantly increased compared with controls. In contrast to increased mean RT, the distributional parameter mu did not document a significant slowing in aADHD. However, subjects with aADHD were characterized by increased IIV throughout the entire RT distribution as indicated by the parameters sigma and tau as well as the SD of reaction time. Moreover, we found a significant correlation between tau and the number of omission errors. Our findings question a primacy of inhibitory deficits in aADHD and provide evidence for attentional dysfunction. The present findings may have theoretical implications for etiological models of ADHD as well as more practical implications for neuropsychological testing in aADHD.", "Although a broad array of neurocognitive dysfunctions are associated with ADHD, it is unknown whether these dysfunctions play a role in the course of ADHD symptoms. The present longitudinal study investigated whether neurocognitive functions assessed at study-entry (mean age = 11.5 years, SD = 2.7) predicted ADHD symptom severity and overall functioning 6 years later (mean age = 17.4 years, 82.6 % = male) in a carefully phenotyped large sample of 226 Caucasian participants from 182 families diagnosed with ADHD-combined type. Outcome measures were dimensional measures of ADHD symptom severity and the Kiddie-Global Assessment Scale (K-GAS) for overall functioning. Predictors were derived from component scores for 8 domains of neurocognitive functioning: working memory, motor inhibition, cognitive inhibition, reaction time variability, timing, information processing speed, motor control, intelligence. Effects of age, gender, and pharmacological treatment were considered. Results showed that better working memory predicted lower ADHD symptom severity (R 2 = 3.0 %), and less reaction time variability predicted better overall functioning (higher K-GAS-score, R 2 = 5.6 %). Predictors were still significant with baseline behavior included in the models. The role of neurocognitive functioning in the long term outcome of ADHD behavior is discussed.", "Reading comprehension is a very complex task that requires different cognitive processes and reading abilities over the life span. There are fewer studies of reading comprehension relative to investigations of word reading abilities. Reading comprehension difficulties, however, have been identified in two common and frequently overlapping childhood disorders: reading disability (RD) and attention-deficit/hyperactivity disorder (ADHD). The nature of reading comprehension difficulties in these groups remains unclear. The performance of four groups of adolescents (RD, ADHD, comorbid ADHD and RD, and normal controls) was compared on reading comprehension tasks as well as on reading rate and accuracy tasks. Adolescents with RD showed difficulties across most reading tasks, although their comprehension scores were average. Adolescents with ADHD exhibited adequate single word reading abilities. Subtle difficulties were observed, however, on measures of text reading rate and accuracy as well as on silent reading comprehension, but scores remained in the average range. The comorbid group demonstrated similar difficulties to the RD group on word reading accuracy and on reading rate but experienced problems on only silent reading comprehension. Implications for reading interventions are outlined, as well as the clinical relevance for diagnosis.", "Intra-individual variability in reaction time (IIV-RT), defined by standard deviation of RT (RTSD), is considered as an endophenotype for attention-deficit/hyperactivity disorder (ADHD). Ex-Gaussian distributions of RT, rather than RTSD, could better characterize moment-to-moment fluctuations in neuropsychological performance. However, data of response variability based on ex-Gaussian parameters as an endophenotypic candidate for ADHD are lacking. We assessed 411 adolescents with clinically diagnosed ADHD based on the DSM-IV-TR criteria as probands, 138 unaffected siblings, and 138 healthy controls. The output parameters, mu, sigma, and tau, of an ex-Gaussian RT distribution were derived from the Conners' continuous performance test. Multi-level models controlling for sex, age, comorbidity, and use of methylphenidate were applied. Compared with unaffected siblings and controls, ADHD probands had elevated sigma value, omissions, commissions, and mean RT. Unaffected siblings formed an intermediate group in-between probands and controls in terms of tau value and RTSD. There was no between-group difference in mu value. Conforming to a context-dependent nature, unaffected siblings still had an intermediate tau value in-between probands and controls across different interstimulus intervals. Our findings suggest IIV-RT represented by tau may be a potential endophenotype for inquiry into genetic underpinnings of ADHD in the context of heterogeneity.", "This study assessed the ability of executive cognitive functioning (ECF) to predict reactive aggression in boys at high and low risk for substance abuse using a 2-year prospective design. ECF is defined as the self-regulation of goal-directed behavior. Reactive aggression involves impulsive hostile reactions committed with little forethought. ECF was measured using five neuropsychological tests in 198 10- to 12-year-old boys with (SA+) and without (SA-) a paternal history of substance abuse/dependence. Reactive aggression was measured, 2 years later, using a composite index of items derived from two self-report measures. It was hypothesized that ECF would predict reactive aggression, and that this relation would be stronger for the SA+ compared with the SA- boys. SA+ subjects demonstrated lower ECF scores and higher reactive aggression scores, compared with SA- controls. ECF predicted reactive aggression in the SA+ group (beta = 0.37, p = 0.001), but not in the SA- group (beta = 0.09, p = NS). This suggests that compromised ECF may be a risk factor for reactive aggression in SA+ youth. The hypothesis that the relation between ECF and reactive aggression is a manifestation of a mild dysfunction of the prefrontal cortex is discussed.", "The letters, numbers, and objects subtests of the Rapid Automatized Naming Tests (RAN) were given to 50 first- and second-grade students. Student performance on the three RAN subtests were audiotaped and subjected to postacquisition processing to distinguish articulation and interarticulation pause times. This study investigated (1) the relations between the articulation and pause durations associated with the 50 stimuli of each RAN subtest and (2) the relations between the pause and articulation latencies of the three RAN subtests and reading. For both first- and second-grade students, pause and articulation times for RAN letters and objects were not found to be reliably related, in contrast to RAN numbers articulation and pause durations. RAN subtest pause durations were differentially related to reading; however, articulation was rarely related to reading. The RAN letters pause time was the most robust predictor of decoding and reading comprehension, consistently predicting all first- and second-grade measures. Analysis supported the view that reading is predicted by speed of processing associated with letters, not general processing speed." ]
what are b chromosomes	The number of chromosomes carried by an individual species is one of its defining characteristics. Some species, however, can also carry supernumerary chromosomes referred to as B chromosomes. B chromosomes were recently identified in a laboratory stock of	[ "B chromosomes (Bs) are supernumerary, dispensable parts of the nuclear genome, which appear in many different species of eukaryote. So far, Bs have been considered to be genetically inert elements without any functional genes. Our comparative transcriptome analysis and the detection of active RNA polymerase II (RNAPII) in the proximity of B chromatin demonstrate that the Bs of rye (Secale cereale) contribute to the transcriptome. In total, 1954 and 1218 B-derived transcripts with an open reading frame were expressed in generative and vegetative tissues, respectively. In addition to B-derived transposable element transcripts, a high percentage of short transcripts without detectable similarity to known proteins and gene fragments from A chromosomes (As) were found, suggesting an ongoing gene erosion process. In vitro analysis of the A- and B-encoded AGO4B protein variants demonstrated that both possess RNA slicer activity. These data demonstrate unambiguously the presence of a functional AGO4B gene on Bs and that these Bs carry both functional protein coding genes and pseudogene copies. Thus, B-encoded genes may provide an additional level of gene control and complexity in combination with their related A-located genes. Hence, physiological effects, associated with the presence of Bs, may partly be explained by the activity of B-located (pseudo)genes.", "B chromosomes are supernumerary dispensable parts of the karyotype which appear in some individuals of some populations in some species. Often, they have been considered as 'junk DNA' or genomic parasites without functional genes. Due to recent advances in sequencing technologies, it became possible to investigate their DNA composition, transcriptional activity and effects on the host transcriptome profile in detail. Here, we review the most recent findings regarding the gene content of B chromosomes and their transcriptional activities and discuss these findings in the context of comparable biological phenomena, like sex chromosomes, aneuploidy and pseudogenes. Recent data suggest that B chromosomes carry transcriptionally active genic sequences which could affect the transcriptome profile of their host genome. These findings are gradually changing our view that B chromosomes are solely genetically inert selfish elements without any functional genes. This at one side could partly explain the deleterious effects which are associated with their presence. On the other hand it makes B chromosome a nice model for studying regulatory mechanisms of duplicated genes and their evolutionary consequences.", "Repetitive DNA is a major component in most eukaryotic genomes but is ignored in most genome sequencing projects. Here, we report the quantitative composition in repetitive DNA for a supernumerary (B) chromosome, in the migratory locust (Locusta migratoria), by Illumina sequencing of genomic DNA from B-carrying and B-lacking individuals and DNA obtained from a microdissected B chromosome, as well as the physical mapping of some elements. B chromosome DNA of 94.9% was repetitive, in high contrast with the 64.1% of standard (A) chromosomes. B chromosomes are enriched in satellite DNA (satDNA) (65.2% of B-DNA), with a single satellite (LmiSat02-176) comprising 55% of the B. Six satDNAs were visualized by FISH on the B chromosome, and the only A chromosome carrying all these satellites was autosome 9, pointing to this chromosome, along with autosome 8 (which shares histone genes with the B) as putative ancestors of the B chromosome. We found several transposable elements (TEs) showing nucleotidic variation specific to B-carrying individuals, which was also present in B-carrying transcriptomes. Remarkably, an interstitial region of the B chromosome included a 17 kb chimera composed of 29 different TEs, suggesting reiterative TE insertion in this B chromosome region.", "Accessory, supernumerary, or-most simply-B chromosomes, are found in many eukaryotic karyotypes. These small chromosomes do not follow the usual pattern of segregation, but rather are transmitted in a higher than expected frequency. As increasingly being demonstrated by next-generation sequencing (NGS), their structure comprises fragments of standard (A) chromosomes, although in some plant species, their sequence also includes contributions from organellar genomes. Transcriptomic analyses of various animal and plant species have revealed that, contrary to what used to be the common belief, some of the B chromosome DNA is protein-encoding. This review summarizes the progress in understanding B chromosome biology enabled by the application of next-generation sequencing technology and state-of-the-art bioinformatics. In particular, a contrast is drawn between a direct sequencing approach and a strategy based on a comparative genomics as alternative routes that can be taken towards the identification of B chromosome sequences.", "The B-chromosome of maize contains an A-chromosome centromere-specific satellite CentC repeat in its centromere region (CENB) and at multiple locations in its distal heterochromatic regions (BDHs). Because CentC is highly repetitive, it is a challenge to study CentC sequences within individual centromeres or chromosome regions. The combined structure of CentC and a BDH-specific CL-repeat has allowed us to isolate CentC sequences from BDHs. In the study described herein, we have used a PCR method to amplify 13 CL-CentC variant products that were specifically mapped to A-centromeres (CENAs), the CENB, and BDHs via the tertiary trisomes and hypoploids of five B-10L translocations. Cloning and sequence analyses of these CL-CentC products have revealed a local CentC homogenization within the three CentC-containing regions. Phylogenetic analysis has indicated that the CentC sequences of BDHs are more closely related to those of CENAs in comparison to that of the CENB. Furthermore, the CentC monomers that are within the CENB are more diverse than those within BDHs and CENAs. These results shed light on the evolution of CentC repeats on the B-chromosome and provide a better understanding of B-chromosome evolution.", "We analyzed the DNA amount in X and B chromosomes of 2 XX/X0 grasshopper species (Eyprepocnemis plorans and Locusta migratoria), by means of Feulgen image analysis densitometry (FIAD), using previous estimates in L. migratoria as standard (5.89 pg). We first analyzed spermatids of 0B males and found a bimodal distribution of integrated optical densities (IODs), suggesting that one peak corresponded to +X and the other to -X spermatids. The difference between the 2 peaks corresponded to the X chromosome DNA amount, which was 1.28 pg in E. plorans and 0.80 pg in L. migratoria. In addition, the +X peak in E. plorans gave an estimate of the C-value in this species (10.39 pg). We next analyzed diplotene cells from 1B males in E. plorans and +B males in L. migratoria (a species where Bs are mitotically unstable and no integer B number can be defined for an individual) and measured B chromosome IOD relative to X chromosome IOD, within the same cell, taking advantage of the similar degree of condensation for both positively heteropycnotic chromosomes at this meiotic stage. From this proportion, we estimated the DNA amount for 3 different B chromosome variants found in individuals from 3 E. plorans Spanish populations (0.54 pg for B1 from Saladares, 0.51 pg for B2 from Salobreña and 0.64 for B24 from Torrox). Likewise, we estimated the DNA amount of the B chromosome in L. migratoria to be 0.15 pg. To automate measurements, we wrote a GPL3 licensed Python program (pyFIA). We discuss the utility of the present approach for estimating X and B chromosome DNA amount in a variety of situations, and the meaning of the DNA amount estimates for X and B chromosomes in these 2 species.", "Drosophila melanogaster Polo kinase physically interacts with, and is repressed by, the Matrimony (Mtrm) protein during oogenesis. Females heterozygous for a deletion of the mtrm gene display defects in chromosome segregation at meiosis I. However, a complete absence of Mtrm results in both meiotic catastrophe and female sterility. We show that three phosphorylated residues in an N-terminal region in Mtrm are required for Mtrm::Polo binding. However, this binding is noncanonical; it does not require either a complete S-pS/pT-P motif in Mtrm or key residues in the Polo-box domain of Polo that allow Polo to bind phosphorylated substrates. By using fluorescence cross-correlation spectroscopy to characterize the Mtrm::Polo interaction in vivo, we show that a sterile α-motif (SAM) domain located at the C terminus of Mtrm increases the stability of Mtrm::Polo binding. Although Mtrm's C-terminal SAM domain is not required to rescue the chromosome segregation defects observed in mtrm/+ females, it is essential to prevent both meiotic catastrophe and the female sterility observed in mtrm/mtrm females. We propose that Polo's interaction with the cluster of phosphorylated residues alone is sufficient to rescue the meiosis I defect. However, the strengthening of Mtrm::Polo binding mediated by the SAM domain is necessary to prevent meiotic catastrophe and ensure female fertility. Characterization of the Mtrm::Polo interaction, as well as that of other Polo regulators, may assist in the design of a new class of Polo inhibitors to be used as targeted anticancer therapeutic agents.", "Organization of B chromosomes in the Korean field mouse Apodemus peninsulae was analyzed. We painted its metaphase chromosomes with whole and partial chromosome paints generated by microdissection and DOP-PCR. The results of the painting indicated that all B chromosomes contained a large amount of repeated DNA sequences. The repeats could be classified in terms of their homology and predominant location. Pericentromeric repeats of B chromosomes were present in many copies in pericentromeric C-blocks of all autosomes and in non-centromeric C-blocks of the sex chromosomes. B arm specific type 1 repeats comprised the main body of the arms of almost all B chromosomes and were present in the arms of A chromosomes as interspersed sequences. B arm-specific type 2 repeats were found at the ends of some B chromosomes that did not undergo compaction at the interphase- metaphase transition and remained uncondensed. On the basis of comparative analysis of localization of B chromosome repeats in the chromosomes of two related species, A. peninsulae and A. agrarius, we suggest a hypothesis of B chromosome origin and evolution in the genus Apodemus.", "Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes that cannot be unambiguously identified by banding cytogenetics. The objective of this study was to provide an overview of sSMC frequency and characterization in a context of infertility and to review the literature describing sSMC in relation with male and female infertility. Therefore, a systematic literature review on sSMC associated with infertility was conducted by means of a PubMed literature and a sSMC database (http://ssmc-tl.com/sSMC.html) search. A total of 234 patients with infertility were identified as carriers of sSMC. All chromosomes, except chromosomes 10, 19 and the X, were involved in sSMC, and in 72% the sSMC originated from acrocentric chromosomes. Euchromatic imbalances were caused by the presence of sSMC in 30% of the cases. Putative genes have been identified in only 1.2% of sSMC associated with infertility. The implication of sSMC in infertility could be due to a partial trisomy of some genes but also to mechanical effects perturbing meiosis. Further precise molecular and interphase-architecture studies on sSMC are needed in the future to characterize the relationship between this chromosomal anomaly and human infertility.", "In Plantagolagopus the B chromosome has been reported by our laboratory to be the result of massive amplification of ribosomal DNA sequences. However, the presence of transposable elements and other repetitive DNA sequences together with rDNA could not be ruled out. The present study clearly demonstrated the presence of transposable elements in the B chromosomes. These transposable elements were characterized and their nature assessed. Physical mapping using double fluorescent in situ hybridization was performed using DNA probes for 5S and copia elements. The results clearly proved that the B chromosome is a mix of 5S, 45S rDNA and transposable elements. Based on the FISH and Fiber-FISH patterns, it can be concluded that while 45S rDNA sequences are restricted to the subtelomeric regions, the 5S rDNA sequences are interspersed with transposons in the body of the B chromosome. These results have further enhanced our understanding of the organization and evolution of B chromosomes." ]
Quality of time-of-flight MR angiography with venous suppression at 7T on imaging superficial temporal artery	To evaluate the quality of time-of-flight MR angiography (TOF-MRA) with venous suppression at 7T on imaging superficial temporal artery (STA).	[ "Continuous arterial spin-labeled perfusion MRI (CASL-PI) uses electromagnetically labeled arterial blood water as a diffusible tracer to noninvasively measure cerebral blood flow (CBF). We hypothesized that CASL-PI could detect perfusion deficits and perfusion/diffusion mismatches and predict outcome in acute ischemic stroke. We studied 15 patients with acute ischemic stroke within 24 hours of symptom onset. With the use of a 6-minute imaging protocol, CASL-PI was measured at 1.5 T in 8-mm contiguous supratentorial slices with a 3.75-mm in-plane resolution. Diffusion-weighted images were also obtained. Visual inspection for perfusion deficits, perfusion/diffusion mismatches, and effects of delayed arterial transit was performed. CBF in predetermined vascular territories was quantified by transformation into Talairach space. Regional CBF values were correlated with National Institutes of Health Stroke Scale (NIHSS) score on admission and Rankin Scale (RS) score at 30 days. Interpretable CASL-PI images were obtained in all patients. Perfusion deficits were consistent with symptoms and/or diffusion-weighted imaging abnormalities. Eleven patients had hypoperfusion, 3 had normal perfusion, and 1 had relative hyperperfusion. Perfusion/diffusion mismatches were present in 8 patients. Delayed arterial transit effect was present in 7 patients; serial imaging in 2 of them showed that the delayed arterial transit area did not succumb to infarction. CBF in the affected hemisphere correlated with NIHSS and RS scores (P=0.037 and P=0.003, Spearman rank correlation). The interhemispheric percent difference in middle cerebral artery CBF correlated with NIHSS and RS scores (P=0.007 and P=0.0002, respectively). CASL-PI provides rapid noninvasive multislice imaging in acute ischemic stroke. It depicts perfusion deficits and perfusion/diffusion mismatches and quantifies regional CBF. CASL-PI CBF asymmetries correlate with severity and outcome. Delayed arterial transit effects may indicate collateral flow.", "Prompt diagnosis of vessel pathology and appropriate treatment of moyamoya vasculopathy (MMV) are essential to improve long-term prognosis. The aims of our study were to explore the diagnostic value of ultra-high-field (UHF) magnetic resonance imaging at 7.0 T in MMV patients and to compare the applicability of two different 7.0 T vessel imaging modalities to 3.0 T magnetic resonance angiography (MRA) and digital subtraction angiography (DSA). In a World Health Organization-registered and prospective imaging trial, patients were investigated at 7.0 T magnetization-prepared rapid-acquisition gradient echo (MPRAGE)-MRA and time-of-flight (TOF)-MRA, 3.0 T TOF-MRA, and by DSA. Six patients were included in our study and evaluated for MMV. 3.0 T TOF-MRA and 7.0 T MPRAGE-MRA were able to depict the complete major vascular tree and confirmed MMV-specific steno-occlusions of major intracranial arteries, as previously identified by DSA. 7.0 T TOF-MRA was limited to visualization of the circle of Willis as well as the internal carotid artery only. Donor vessels for bypass surgery (i.e., branches of superficial temporal artery) could be sufficiently visualized with all magnetic resonance modalities. Our results indicate that a specific 7.0 T vascular imaging protocol yields diagnostic information about vessel pathology in MMV that approximates conventional DSA. 7.0 T MPRAGE was superior to 7.0 T TOF-MRA due to shorter scanning times and better brain coverage. To date, however, limited availability of 7.0 T technology in medical facilities as well as technical and procedural constraints excludes a fair amount of patients from the clinical 7.0 T imaging process.", "Conventional saturation pulses cannot be used for 7 Tesla ultra-high-resolution time-of-flight magnetic resonance angiography (TOF MRA) due to specific absorption rate (SAR) limitations. We overcome these limitations by utilizing low flip angle, variable rate selective excitation (VERSE) algorithm saturation pulses. Twenty-five neurosurgical patients (male n = 8, female n = 17; average age 49.64 years; range 26-70 years) with different intracranial vascular pathologies were enrolled in this trial. All patients were examined with a 7 Tesla (Magnetom 7 T, Siemens) whole body scanner system utilizing a dedicated 32-channel head coil. For venous saturation pulses a 35° flip angle was applied. Two neuroradiologists evaluated the delineation of arterial vessels in the Circle of Willis, delineation of vascular pathologies, presence of artifacts, vessel-tissue contrast and overall image quality of TOF MRA scans in consensus on a five-point scale. Normalized signal intensities in the confluence of venous sinuses, M1 segment of left middle cerebral artery and adjacent gray matter were measured and vessel-tissue contrasts were calculated. Ratings for the majority of patients ranged between good and excellent for most of the evaluated features. Venous saturation was sufficient for all cases with minor artifacts in arteriovenous malformations and arteriovenous fistulas. Quantitative signal intensity measurements showed high vessel-tissue contrast for confluence of venous sinuses, M1 segment of left middle cerebral artery and adjacent gray matter. The use of novel low flip angle VERSE algorithm pulses for saturation of venous vessels can overcome SAR limitations in 7 Tesla ultra-high-resolution TOF MRA. Our protocol is suitable for clinical application with excellent image quality for delineation of various intracranial vascular pathologies.", "The purpose of this study was to evaluate the feasibility of MR angiography (MRA) at 7.0 Tesla (T) using optimized birdcage (BC) coils with simple end cap configurations. Shielded 16-rung high-pass BC coils were built with identical geometry and compared with different sizes and locations of end caps. To determine whether the end cap configuration was effective, the signal intensity profiles along the superior-inferior (S-I) direction were analyzed in phantom and in vivo human experiments. The effects were also investigated in two-dimensional (2D) and three-dimensional (3D) time-of-flight (TOF) MRA experiments. The signal intensity profiles showed that B1 homogeneity at the service end, that is, the end cap side, was improved as the diameter of the end caps increased and the end cap became closer to the coil end ring. The results of 2D and 3D TOF experiments showed the best improvement of vessel visibility at the BC coil with an 80% end cap, when compared with BC coils with other end cap sizes or without an end cap. In conclusion, the BC coil with an end cap was effective for improving S-I directional homogeneity and suitable for MRA applications, especially at ultrahigh field MRI, such as 7.0T." ]
Cardiac fibroblast-specific activating transcription factor 3 affects cardiac repair after myocardial infarction	Myocardial ischemia injury is one of the leading causes of death and disability worldwide. Cardiac fibroblasts (CFs) have central roles in modulating cardiac function under pathophysiological conditions. Activating transcription factor 3 (ATF3) plays a self-protective role in counteracting CF dysfunction. However, the precise function of CF-specific ATF3 during myocardial infarction (MI) injury/repair remains incompletely understood. The aim of this study was to determine whether CF-specific ATF3 affected cardiac repair after MI.	[ "Cardiac fibroblasts form one of the largest cell populations, in terms of cell numbers, in the heart. They contribute to structural, biochemical, mechanical and electrical properties of the myocardium. Nonetheless, they are often disregarded by in vivo and in vitro studies into cardiac function. This review summarizes our understanding of fibroblast origin and identity, their structural organization and role in myocardial architecture, as well as functional aspects related to cell signalling and electro-mechanical function in the heart.", "The volume overload of isolated mitral regurgitation (MR) in the dog results in left ventricular (LV) dilatation and interstitial collagen loss. To better understand the mechanism of collagen loss, we performed a gene array and overlaid regulated genes into ingenuity pathway analysis. Gene arrays from LV tissue were compared in 4 dogs before and 4 months after MR. Cine-magnetic resonance-derived LV end-diastolic volume increased 2-fold (P=0.005), and LV ejection fraction increased from 41% to 53% (P<0.007). LV interstitial collagen decreased 40% (P<0.05) compared with controls, and replacement collagen was in short strands and in disarray. Ingenuity pathway analysis identified Marfan syndrome, aneurysm formation, LV dilatation, and myocardial infarction, all of which have extracellular matrix protein defects and/or degradation. Matrix metalloproteinase-1 and -9 mRNA increased 5- (P=0.01) and 10-fold (P=0.003), whereas collagen I did not change and collagen III mRNA increased 1.5-fold (P=0.02). However, noncollagen genes important in extracellular matrix structure were significantly downregulated, including decorin, fibulin 1, and fibrillin 1. In addition, connective tissue growth factor and plasminogen activator inhibitor were downregulated, along with multiple genes in the transforming growth factor-beta signaling pathway, resulting in decreased LV transforming growth factor-beta1 activity (P=0.03). LV collagen loss in isolated, compensated MR is chiefly due to posttranslational processing and degradation. The downregulation of multiple noncollagen genes important in global extracellular matrix structure, coupled with decreased expression of multiple profibrotic factors, explains the failure to replace interstitial collagen in the MR heart.", "The cholesterol-lowering statin drugs have some non-lipid-lowering effects, such as inhibiting myocardial remodeling. However, the underlying mechanism is still unclear. The left anterior descending coronary artery was ligated to establish a rat model of heart failure, and the rats were divided into a sham operation (SO) group, myocardial infarction model (MI) group, and MI-atorvastatin group. Changes in hemodynamic parameters were recorded after the final drug administration. Histological diagnosis was made by reviewing hematoxylin and eosin (HE) stained tissue. Real-time quantitative polymerase chain reaction (PCR) was performed to determine the expressions of type I and type III collagen, matrix metalloproteinase-2 (MMP-2), and tissue matrix metalloproteinase inhibitor-2 (TIMP-2). Further, primary rat cardiac fibroblasts were cultured and the MTT assay was performed to determine the effect of atorvastatin on cardiac fibroblast proliferation. The model of heart failure was established and the results of HE staining and Masson's trichrome staining revealed that the rats in the heart failure group showed obvious hyperplasia of fibrotic tissue, which was significantly reduced in the atorvastatin group. Real-time quantitative PCR showed that the MI group showed a significantly increased expression of type I and type III collagen, MMP-2, and TIMP-2, but a significantly reduced MMP-2/TIMP-2 ratio. Compared with the MI group, the atorvastatin group showed significantly reduced expression of type I and III collagen, unchanged expression of MMP-2, significantly reduced expression of TIMP-2, and an increased MMP-2/TIMP-2 ratio. We further found that atorvastatin significantly inhibited the Ang II-induced fibroblast proliferation and the expression of type I and type III collagen in cardiac fibroblasts while increasing the MMP-2/TIMP-2 ratio. These data suggest that atorvastatin can inhibit cardiac fibroblast proliferation and enhance collagen degradation by increasing the MMP-2/TIMP-2 ratio, thereby inhibiting the formation of myocardial fibrosis in rats with heart failure after myocardial infarction.", "Myocardial infarction (MI) is followed by extracellular matrix (ECM) remodeling, which is on the one hand required for the healing response and the formation of stable scar tissue. However, on the other hand, ECM remodeling can lead to fibrosis and decreased ventricular compliance. The small leucine-rich proteoglycan (SLRP), biglycan (bgn), has been shown to be critically involved in these processes. During post-infarct remodeling cardiac fibroblasts differentiate into myofibroblasts which are the main cell type mediating ECM remodeling. The aim of the present study was to characterize the role of bgn in modulating the phenotype of cardiac fibroblasts. Cardiac fibroblasts were isolated from hearts of wild-type (WT) versus bgn(-/0) mice. Phenotypic characterization of the bgn(-/0) fibroblasts revealed increased proliferation. Importantly, this phenotype of bgn(-/0) fibroblasts was abolished to the WT level by reconstitution of biglycan in the ECM. TGF-β receptor II expression and phosphorylation of SMAD2 were increased. Furthermore, indicative of a myofibroblast phenotype bgn(-/0) fibroblasts were characterized by increased α-smooth muscle actin (α-SMA) incorporated into stress fibers, increased formation of focal adhesions, and increased contraction of collagen gels. Administration of neutralizing antibodies to TGF-β reversed the pro-proliferative, myofibroblastic phenotype. In vivo post-MI α-SMA, TGF-β receptor II expression, and SMAD2 phosphorylation were markedly increased in bgn(-/0) mice. Collectively, the data suggest that bgn deficiency promotes myofibroblast differentiation and proliferation in vitro and in vivo likely due to increased responses to TGF-β and SMAD2 signaling.", "Hypertensive ventricular remodeling is a common cause of heart failure. However, the molecular mechanisms regulating ventricular remodeling remain poorly understood. We used a discovery-driven/nonbiased approach to identify increased activating transcription factor 3 (ATF3) expression in hypertensive heart. We used loss/gain of function approaches to understand the role of ATF3 in heart failure. We also examined the mechanisms through transcriptome, chromatin immunoprecipitation sequencing analysis, and in vivo and in vitro experiments. ATF3 expression increased in murine hypertensive heart and human hypertrophic heart. Cardiac fibroblast cells are the primary cell type expressing high ATF3 levels in response to hypertensive stimuli. ATF3 knockout (ATF3KO) markedly exaggerated hypertensive ventricular remodeling, a state rescued by lentivirus-mediated/miRNA-aided cardiac fibroblast-selective ATF3 overexpression. Conversely, conditional cardiac fibroblast cell-specific ATF3 transgenic overexpression significantly ameliorated ventricular remodeling and heart failure. We identified Map2K3 as a novel ATF3 target. ATF3 binds with the Map2K3 promoter, recruiting HDAC1, resulting in Map2K3 gene-associated histone deacetylation, thereby inhibiting Map2K3 expression. Genetic Map2K3 knockdown rescued the profibrotic/hypertrophic phenotype in ATF3KO cells. Last, we demonstrated that p38 is the downstream molecule of Map2K3 mediating the profibrotic/hypertrophic effects in ATF3KO animals. Inhibition of p38 signaling reduced transforming growth factor-β signaling-related profibrotic and hypertrophic gene expression, and blocked exaggerated cardiac remodeling in ATF3KO cells. Our study provides the first evidence that ATF3 upregulation in cardiac fibroblasts in response to hypertensive stimuli protects the heart by suppressing Map2K3 expression and subsequent p38-transforming growth factor-β signaling. These results suggest that positive modulation of cardiac fibroblast ATF3 may represent a novel therapeutic approach against hypertensive cardiac remodeling.", "Fibroblasts do not only serve as matrix-producing reparative cells, but exhibit a wide range of functions in inflammatory and immune responses, angiogenesis and neoplasia. The adult mammalian myocardium contains abundant fibroblasts enmeshed within the interstitial and perivascular extracellular matrix. The current review manuscript discusses the dynamic phenotypic and functional alterations of cardiac fibroblasts following myocardial infarction. Extensive necrosis of cardiomyocytes in the infarcted heart triggers an intense inflammatory reaction. In the early stages of infarct healing, fibroblasts become pro-inflammatory cells, activating the inflammasome and producing cytokines, chemokines and proteases. Pro-inflammatory cytokines (such as Interleukin-1) delay myofibroblast transformation, until the wound is cleared from dead cells and matrix debris. Resolution of the inflammatory infiltrate is associated with fibroblast migration, proliferation, matrix protein synthesis and myofibroblast conversion. Growth factors and matricellular proteins play an important role in myofibroblast activation during the proliferative phase of healing. Formation of a mature cross-linked scar is associated with clearance of fibroblasts, as poorly-understood inhibitory signals restrain the fibrotic response. However, in the non-infarcted remodeling myocardium, local fibroblasts may remain activated in response to volume and pressure overload and may promote interstitial fibrosis. Considering their abundance, their crucial role in cardiac inflammation and repair, and their involvement in myocardial dysfunction and arrhythmogenesis, cardiac fibroblasts may be key therapeutic targets in cardiac remodeling. This article is part of a Special Issue entitled Myocyte-Fibroblast Signalling in Myocardium.", "Myocardial TGF-β expression is upregulated in experimental models of myocardial infarction and cardiac hypertrophy, and in patients with dilated or hypertrophic cardiomyopathy. Through its effects on cardiomyocytes, mesenchymal and immune cells, TGF-β plays an important role in the pathogenesis of cardiac remodeling and fibrosis. TGF-β overexpression in the mouse heart is associated with fibrosis and hypertrophy. Endogenous TGF-β plays an important role in the pathogenesis of cardiac fibrotic and hypertrophic remodeling, and modulates matrix metabolism in the pressure-overloaded heart. In the infarcted heart, TGF-β deactivates inflammatory macrophages, while promoting myofibroblast transdifferentiation and matrix synthesis through Smad3-dependent pathways. Thus, TGF-β may serve as the \"master switchThis article is part of a special issue entitled \"Key Signaling Molecules in Hypertrophy and Heart Failure\". for the transition of the infarct from the inflammatory phase to formation of the scar. Because of its crucial role in cardiac remodeling, the TGF-β system may be a promising therapeutic target for patients with heart failure. However, efforts to translate these concepts into therapeutic strategies, in order to prevent cardiac hypertrophy and fibrosis, are hampered by the complex, pleiotropic and diverse effects of TGF-β signaling, by concerns regarding deleterious actions of TGF-β inhibition and by the possibility of limited benefit in patients receiving optimal treatment with ACE inhibitors and β-adrenergic blockers. Dissection of the pathways responsible for specific TGF-β-mediated actions and understanding of cell-specific actions of TGF-β are needed to design optimal therapeutic strategies. This article is part of a special issue entitled \"Key Signaling Molecules in Hypertrophy and Heart Failure\"." ]
Is there a way to create a non-typeable query?	Nontypeable	[ "Nontypeable Haemophilus influenzae (NTHi) is a gram-negative bacterium and a common commensal organism of the upper respiratory tract in humans. NTHi causes a number of diseases, including otitis media, sinusitis, conjunctivitis, exacerbations of chronic obstructive pulmonary disease, and bronchitis. During the course of colonization and infection, NTHi must withstand oxidative stress generated by insult due to multiple reactive oxygen species produced endogenously by other copathogens and by host cells. Using an NTHi-specific microarray containing oligonucleotides representing the 1821 open reading frames of the recently sequenced NTHi isolate 86-028NP, we have identified 40 genes in strain 86-028NP that are upregulated after induction of oxidative stress due to hydrogen peroxide. Further comparisons between the parent and an isogenic oxyR mutant identified a subset of 11 genes that were transcriptionally regulated by OxyR, a global regulator of oxidative stress. Interestingly, hydrogen peroxide induced the OxyR-independent upregulation of expression of the genes encoding components of multiple iron utilization systems. This finding suggested that careful balancing of levels of intracellular iron was important for minimizing the effects of oxidative stress during NTHi colonization and infection and that there are additional regulatory pathways involved in iron utilization.", "Nontypeable Haemophilus influenzae (NTHI) is a common commensal and opportunistic pathogen of the human airways. For example, NTHI is a leading cause of otitis media and is the most common cause of airway infections associated with chronic obstructive pulmonary disease (COPD). These infections are often chronic/recurrent in nature and involve bacterial persistence within biofilm communities that are highly resistant to host clearance. Our previous work has shown that NTHI within biofilms has increased expression of factors associated with oxidative stress responses. The goal of this study was to define the roles of catalase (encoded by hktE) and a bifunctional peroxiredoxin-glutaredoxin (encoded by pdgX) in resistance of NTHI to oxidants and persistence in vivo. Isogenic NTHI strain 86-028NP mutants lacking hktE and pdgX had increased susceptibility to peroxide. Moreover, these strains had persistence defects in the chinchilla infection model for otitis media, as well as in a murine model for COPD. Additional work showed that pdgX and hktE were important determinants of NTHI survival within neutrophil extracellular traps (NETs), which we have shown to be an integral part of NTHI biofilms in vivo. Based on these data, we conclude that catalase and peroxiredoxin-glutaredoxin are determinants of bacterial persistence during chronic/recurrent NTHI infections that promote bacterial survival within NETs.", "Nontypeable Haemophilus influenzae (NTHI) is an important pathogen in respiratory tract infections, including otitis media (OM). NTHI forms biofilms in vitro as well as in the chinchilla middle ear, suggesting that biofilm formation in vivo might play an important role in the pathogenesis and chronicity of OM. We've previously shown that SiaA, SiaB, and WecA are involved in biofilm production by NTHI in vitro. To investigate whether these gene products were also involved in biofilm production in vivo, NTHI strain 2019 and five isogenic mutants with deletions in genes involved in carbohydrate biosynthesis were inoculated into the middle ears of chinchillas. The wild-type strain formed a large, well-organized, and viable biofilm; however, the wecA, lsgB, siaA, pgm, and siaB mutants were either unable to form biofilms or formed biofilms of markedly reduced mass, organization, and viability. Despite their compromised ability to form a biofilm in vivo, wecA, lsgB, and siaA mutants survived in the chinchilla, inducing culture-positive middle ear effusions, whereas pgm and siaB mutants were extremely sensitive to the bactericidal activity of chinchilla serum and thus did not survive. Lectin analysis indicated that sialic acid was an important component of the NTHI 2019 biofilm produced in vivo. Our data suggested that genes involved in carbohydrate biosynthesis and assembly play an important role in the ability of NTHI to form a biofilm in vivo. Collectively, we found that when modeled in a mammalian host, whereas biofilm formation was not essential for survivability of NTHI in vivo, lipooligosaccharide sialylation was indispensable.", "Complete bacterial genomic DNA sequences have allowed application of genome-scale strategies to identify essential genes. Efficient generation of conditional loss of function mutations provides a means of characterization of this class of genes. Promoter systems conferring tight regulation are particularly applicable to generating such mutations and we sought to apply this approach for the analysis of an essential gene of Haemophilus influenzae. Therefore, we developed the use of a D-xylose-inducible promoter for verification of an essential role in growth for yraM, which encodes a putative periplasmic lipoprotein, in both H. influenzae Rd and virulent type b strains. This promoter was sufficiently tightly regulated to generate conditionally viable strains by inducible expression of YraM. A second approach was used to further characterize YraM. Natural transformation and an ordered mutant collection spanning the H. influenzae genome provide the means to target any gene of interest for mutagenesis and temperature-sensitive (TS) mutant isolation. This strategy was applied to generate a conditionally lethal allele of yraM. The resulting TS mutation was directly mapped to a single amino acid substitution within a motif conserved in all putative YraM orthologs and this mutation was shown to be sufficient to confer the TS phenotype.", "Otitis media (OM) is among the leading diseases of childhood and is caused by opportunists that reside within the nasopharynx, such as Haemophilus influenzae and Moraxella catarrhalis. As with most airway infections, it is now clear that OM infections involve multiple organisms. This study addresses the hypothesis that polymicrobial infection alters the course, severity, and/or treatability of OM disease. The results clearly show that coinfection with H. influenzae and M. catarrhalis promotes the increased resistance of biofilms to antibiotics and host clearance. Using H. influenzae mutants with known biofilm defects, these phenotypes were shown to relate to biofilm maturation and autoinducer-2 (AI-2) quorum signaling. In support of the latter mechanism, chemically synthesized AI-2 (dihydroxypentanedione [DPD]) promoted increased M. catarrhalis biofilm formation and resistance to antibiotics. In the chinchilla infection model of OM, polymicrobial infection promoted M. catarrhalis persistence beyond the levels seen in animals infected with M. catarrhalis alone. Notably, no such enhancement of M. catarrhalis persistence was observed in animals infected with M. catarrhalis and a quorum signaling-deficient H. influenzae luxS mutant strain. We thus conclude that H. influenzae promotes M. catarrhalis persistence within polymicrobial biofilms via interspecies quorum signaling. AI-2 may therefore represent an ideal target for disruption of chronic polymicrobial infections. Moreover, these results strongly imply that successful vaccination against the unencapsulated H. influenzae strains that cause airway infections may also significantly impact chronic M. catarrhalis disease by removing a reservoir of the AI-2 signal that promotes M. catarrhalis persistence within biofilm.", "Evidence is mounting that nontypeable Haemophilus influenzae grows as a biofilm in the middle ear of children with otitis media and the airways of adults with chronic obstructive pulmonary disease. To begin to assess antigens expressed by H. influenzae in biofilms, cell envelopes of bacteria grown as a biofilm were compared to those grown planktonically. A approximately 30kDa peroxiredoxin-glutaredoxin was present in greater abundance during growth in biofilms. Mutants deficient in expression of peroxiredoxin-glutaredoxin were constructed by homologous recombination in four clinical isolates. The mutants showed a 25-50% reduction in biofilm formation compared to the corresponding parent strains. To study in vivo expression of peroxiredoxin-glutaredoxin during human respiratory tract infection, paired pre- and post-exacerbation serum from adults with chronic obstructive pulmonary disease and H. influenzae in sputum were assayed using an enzyme-linked immunosorbent assay and purified recombinant peroxiredoxin-glutaredoxin. Eight from 18 (44.4%) paired serum samples showed a significant increase in antibody to peroxiredoxin-glutaredoxin from pre- to post-infection. These results indicate that (1) peroxiredoxin-glutaredoxin is present in greater abundance in H. influenzae biofilms compared to planktonically grown bacteria; (2) peroxiredoxin-glutaredoxin is involved in biofilm formation by H. influenzae and the degree of involvement varies among strains; and (3) peroxiredoxin-glutaredoxin is expressed by H. influenzae during infection of the human respiratory tract and is recognized by the human immune system.", "Increased bacterial concentration (load) in the lower airways and new bacterial strain acquisition have been posited as mechanisms for chronic obstructive pulmonary disease (COPD) exacerbations. Bacterial concentrations are higher during exacerbation than during stable disease; however, these studies are cross sectional and devoid of strain typing. To determine if the increased bacterial concentrations function as a separate mechanism for exacerbation induction independent of new strain acquisition. In a prospective, longitudinal cohort of patients with COPD, the relationship between exacerbation occurrence, sputum bacterial concentrations, and new strain acquisition was examined. Clinical information, quantitative sputum cultures, and molecular typing of potential bacterial pathogen isolates. Over 81 months, 104 subjects completed 3,009 clinic visits, 560 (19.6%) during exacerbations and 2,449 (80.4%) during stable disease. Among preexisting strains, sputum concentrations of Nontypeable Haemophilus influenzae and Haemophilus haemolyticus were not different in exacerbation versus stable disease. Moraxella catarrhalis (stable, 10(8.38 +/- 0.13) [mean +/- SEM] vs. exacerbation, 10(7.78 +/- 0.26); p = 0.02) and Streptococcus pneumoniae (stable, 10(8.42 +/- 0.21) vs. exacerbation, 10(7.76 +/- 0.52); p = 0.07) concentrations were lower during exacerbations compared with stable periods. Concentrations of new strains of H. influenzae (stable, 10(7.28 +/- 0.15) vs. exacerbation, 10(7.76 +/- 0.17); p = 0.04) and M. catarrhalis (stable, 10(7.85 +/- 0.15) vs. exacerbation, 10(8.37 +/- 0.14); p = 0.02), were increased during exacerbations; however, the differences were small. Change in bacterial load is unlikely to be an important mechanism for exacerbations. Better understanding of the host-pathogen interaction, rather than enumerating bacteria in respiratory samples, is required to provide new insights into bacterial infection in COPD." ]
Ex vivo expanded HIV-specific T cells: a phase 1 study	Adoptive T cell therapy has had dramatic successes in the treatment of virus-related malignancies and infections following hematopoietic stem cell transplantation. We adapted this method to produce ex vivo expanded HIV-specific T cells (HXTCs), with the long-term goal of using HXTCs as part of strategies to clear persistent HIV infection. In this phase 1 proof-of-concept study (NCT02208167), we administered HXTCs to antiretroviral therapy (ART)-suppressed, HIV-infected participants. Participants received two infusions of 2 × 10	[ "There is a need to develop improved methods to treat and potentially cure HIV infection. During chronic HIV infection, replication is concentrated within T follicular helper cells (Tfh) located within B cell follicles, where low levels of virus-specific CTL permit ongoing viral replication. We previously showed that elevated levels of simian immunodeficiency virus (SIV)-specific CTL in B cell follicles are linked to both decreased levels of viral replication in follicles and decreased plasma viral loads. These findings provide the rationale to develop a strategy for targeting follicular viral-producing (Tfh) cells using antiviral chimeric antigen receptor (CAR) T cells co-expressing the follicular homing chemokine receptor CXCR5. We hypothesize that antiviral CAR/CXCR5-expressing T cells, when infused into an SIV-infected animal or an HIV-infected individual, will home to B cell follicles, suppress viral replication, and lead to long-term durable remission of SIV and HIV. To begin to test this hypothesis, we engineered gammaretroviral transduction vectors for co-expression of a bispecific anti-SIV CAR and rhesus macaque CXCR5. Viral suppression by CAR/CXCR5-transduced T cells was measured in vitro, and CXCR5-mediated migration was evaluated using both an in vitro transwell migration assay, as well as a novel ex vivo tissue migration assay. The functionality of the CAR/CXCR5 T cells was demonstrated through their potent suppression of SIVmac239 and SIVE660 replication in in vitro and migration to the ligand CXCL13 in vitro, and concentration in B cell follicles in tissues ex vivo. These novel antiviral immunotherapy products have the potential to provide long-term durable remission (functional cure) of HIV and SIV infections.", "Histone deacetylases (HDACs) act on histones within the nucleosome-bound promoter of human immunodeficiency virus type 1 (HIV-1) to maintain proviral latency. HDAC inhibition leads to promoter expression and the escape of HIV from latency. We evaluated the ability of the potent inhibitor recently licensed for use in oncology, suberoylanilide hydroxamic acid (SAHA; Vorinostat), selective for Class I HDACs, to induce HIV promoter expression in cell lines and virus production from the resting CD4(+) T cells of antiretroviral-treated, aviremic HIV-infected patients. In J89, a Jurkat T cell line infected with a single HIV genome encoding the enhanced green fluorescence protein (EGFP) within the HIV genome, SAHA induced changes at nucleosome 1 of the HIV promoter in chromatin immunoprecipitation (ChIP) assays in concert with EGFP expression. In the resting CD4(+) T cells of antiretroviral-treated, aviremic HIV-infected patients clinically achievable exposures to SAHA induced virus outgrowth ex vivo. These results suggest that potent, selective HDAC inhibitors may allow improved targeting of persistent proviral HIV infection, and define parameters for in vivo studies using SAHA.", "Highly active antiretroviral therapy (HAART) suppresses HIV-1 replication but cannot eliminate the virus because HIV-1 establishes latent infection. Interruption of HAART leads to a rapid rebound of viremia, so life-long treatment is required. Efforts to purge the latent reservoir have focused on reactivating latent proviruses without inducing global T cell activation. However, the killing of the infected cells after virus reactivation, which is essential for elimination of the reservoir, has not been assessed. Here we show that after reversal of latency in an in vitro model, infected resting CD4(+) T cells survived despite viral cytopathic effects, even in the presence of autologous cytolytic T lymphocytes (CTLs) from most patients on HAART. Antigen-specific stimulation of patient CTLs led to efficient killing of infected cells. These results demonstrate that stimulating HIV-1-specific CTLs prior to reactivating latent HIV-1 may be essential for successful eradication efforts and should be considered in future clinical trials.", "The capacity of HIV-1 to establish latent infection of CD4+ T cells may allow viral persistence despite immune responses and antiretroviral therapy. Measurements of infectious virus and viral RNA in plasma and of infectious virus, viral DNA and viral messenger RNA species in infected cells all suggest that HIV-1 replication continues throughout the course of infection. Uncertainty remains over what fraction of CD4+ T cells are infected and whether there are latent reservoirs for the virus. We show here that during the asymptomatic phase of infection there is an extremely low total body load of latently infected resting CD4+ T cells with replication-competent integrated provirus (<10(7) cells). The most prevalent form of HIV-1 DNA in resting and activated CD4+ T cells is a full-length, linear, unintegrated form that is not replication competent. The infection progresses even though at any given time in the lymphoid tissues integrated HIV-1 DNA is present in only a minute fraction of the susceptible populations, including resting and activated CD4+ T cells and macrophages." ]
Proteinuric kidney diseases: slit diaphragm proteins, cytoskeletal proteins, and therapeutic options	Proteinuric kidney diseases are a group of disorders with diverse pathological mechanisms associated with significant losses of protein in the urine. The glomerular filtration barrier (GFB), comprised of the three important layers, the fenestrated glomerular endothelium, the glomerular basement membrane (GBM), and the podocyte, dictates that disruption of any one of these structures should lead to proteinuric disease. Podocytes, in particular, have long been considered as the final gatekeeper of the GFB. This specialized visceral epithelial cell contains a complex framework of cytoskeletons forming foot processes and mediate important cell signaling to maintain podocyte health. In this review, we will focus on slit diaphragm proteins such as nephrin, podocin, TRPC6/5, as well as cytoskeletal proteins Rho/small GTPases and synaptopodin and their respective roles in participating in the pathogenesis of proteinuric kidney diseases. Furthermore, we will summarize the potential therapeutic options targeting the podocyte to treat this group of kidney diseases.	[ "Podocytes exhibit a unique cytoskeletal architecture that is fundamentally linked to their function in maintaining the kidney filtration barrier. The cytoskeleton regulates podocyte shape, structure, stability, slit diaphragm insertion, adhesion, plasticity, and dynamic response to environmental stimuli. Genetic mutations demonstrate that even slight impairment of the podocyte cytoskeletal apparatus results in proteinuria and glomerular disease. Moreover, mechanisms underpinning all acquired glomerular pathologies converge on disruption of the cytoskeleton, suggesting that this subcellular structure could be targeted for therapeutic purposes. This review summarizes our current understanding of the function of the cytoskeleton in podocytes and the associated implications for pathophysiology.", "Focal segmental glomerulosclerosis (FSGS) is a syndrome that involves kidney podocyte dysfunction and causes chronic kidney disease. Multiple factors including chemical toxicity, inflammation, and infection underlie FSGS; however, highly penetrant disease genes have been identified in a small fraction of patients with a family history of FSGS. Variants of apolipoprotein L1 (APOL1) have been linked to FSGS in African Americans with HIV or hypertension, supporting the proposal that genetic factors enhance FSGS susceptibility. Here, we used sequencing to investigate whether genetics plays a role in the majority of FSGS cases that are identified as primary or sporadic FSGS and have no known cause. Given the limited number of biopsy-proven cases with ethnically matched controls, we devised an analytic strategy to identify and rank potential candidate genes and used an animal model for validation. Nine candidate FSGS susceptibility genes were identified in our patient cohort, and three were validated using a high-throughput mouse method that we developed. Specifically, we introduced a podocyte-specific, doxycycline-inducible transactivator into a murine embryonic stem cell line with an FSGS-susceptible genetic background that allows shRNA-mediated targeting of candidate genes in the adult kidney. Our analysis supports a broader role for genetic susceptibility of both sporadic and familial cases of FSGS and provides a tool to rapidly evaluate candidate FSGS-associated genes.", "Glucocorticoids exert anti-inflammatory and immunosuppressive activities by genomic and nongenomic effects. The classic genomic effects are mediated by cytosolic glucocorticoid receptors that can upregulate the expression of anti-inflammatory proteins in the nucleus (transactivation) or repress the translocation of proinflammatory transcription factors from the cytosol into the nucleus (transrepression). The nongenomic effects are probably mediated by membrane glucocorticoid receptors. Glucocorticoid receptors are expressed also in podocytes and experimental data suggest that glucocorticoids may protect from podocyte injury. Glucocorticoids have a low therapeutic index and may exert a number of time-dependent and dose-dependent side effects. Measures to prevent or attenuate side effects include single-morning administration of short-acting glucocorticoids, dietetic counseling, increasing physical activity, frequent monitoring, and adapting the doses to the clinical conditions of the patient. Synthetic glucocorticoids, either given alone or in combination with other immunosuppressive drugs, are still the cornerstone therapy in multiple glomerular disorders. However, glucocorticoids are of little benefit in C3 glomerulopathy and may be potentially deleterious in patients with maladaptive focal glomerulosclerosis. Their efficacy depends not only on the type and severity of glomerular disease, but also on the timeliness of administration, the dosage, and the duration of treatment. Whereas an excessive use of glucocorticoids can be responsible for severe toxicity, too low a dosage and too short duration of glucocorticoid treatment can result in false steroid resistance.", "Familial idiopathic nephrotic syndromes represent a heterogeneous group of kidney disorders, and include autosomal recessive steroid-resistant nephrotic syndrome, which is characterized by early childhood onset of proteinuria, rapid progression to end-stage renal disease and focal segmental glomerulosclerosis. A causative gene for this disease, NPHS2, was mapped to 1q25-31 and we report here its identification by positional cloning. NPHS2 is almost exclusively expressed in the podocytes of fetal and mature kidney glomeruli, and encodes a new integral membrane protein, podocin, belonging to the stomatin protein family. We found ten different NPHS2 mutations, comprising nonsense, frameshift and missense mutations, to segregate with the disease, demonstrating a crucial role for podocin in the function of the glomerular filtration barrier.", "Podocyte injury is the inciting event in primary glomerulopathies, such as minimal change disease and primary FSGS, and glucocorticoids remain the initial and often, the primary treatment of choice for these glomerulopathies. Because inflammation is not readily apparent in these diseases, understanding the direct effects of glucocorticoids on the podocyte, independent of the immunomodulatory effects, may lead to the identification of targets downstream of glucocorticoids that minimize toxicity without compromising efficacy. Several studies showed that treatment with glucocorticoids restores podocyte differentiation markers and normal ultrastructure and improves cell survival in murine podocytes. We previously determined that Krüppel-like factor 15 (KLF15), a kidney-enriched zinc finger transcription factor, is required for restoring podocyte differentiation markers in mice and human podocytes under cell stress. Here, we show that in vitro treatment with dexamethasone induced a rapid increase of KLF15 expression in human and murine podocytes and enhanced the affinity of glucocorticoid receptor binding to the promoter region of KLF15 In three independent proteinuric murine models, podocyte-specific loss of Klf15 abrogated dexamethasone-induced podocyte recovery. Furthermore, knockdown of KLF15 reduced cell survival and destabilized the actin cytoskeleton in differentiated human podocytes. Conversely, overexpression of KLF15 stabilized the actin cytoskeleton under cell stress in human podocytes. Finally, the level of KLF15 expression in the podocytes and glomeruli from human biopsy specimens correlated with glucocorticoid responsiveness in 35 patients with minimal change disease or primary FSGS. Thus, these studies identify the critical role of KLF15 in mediating the salutary effects of glucocorticoids in the podocyte.", "The function of glomerular podocytes is closely associated with the actin cytoskeleton. In this study, we studied the role of the small Rho-GTPase, Rac1, in actin organization in podocytes. Conditionally immortalized mouse podocytes (MP) stably expressing nephrin or control plasmid were used. In MP, Rac1 activity increased significantly at 1 week of differentiation. MP stably expressing nephrin showed Rac1 activity significantly higher and more sustained than vector-expressing control cells. Antibody-mediated cross-linking of nephrin also activated Rac1. Differentiated MP showed more distinct lamellipodia/cellular processes, as compared with undifferentiated cells, which was further augmented by nephrin expression. Transient transfection of constitutively active Rac1 markedly increased the number of lamellipodia/cellular processes in undifferentiated MP, while the Rac1 inhibitor caused actin cytoskeleton derangement in differentiating MP. In the rat model of puromycin aminonucleoside nephrosis, RhoA activity was increased at Day 7 (at the peak of proteinuria), while Rac1 activity increased significantly only at Day 14, when the recovery process had started. Rac1 is activated in differentiating MP and nephrin potentiates Rac1 activation. Rac1 likely contributes to lamellipodia formation in differentiating MP and may contribute to process formation in podocytes recovering from injuries.", "Podocytes of the renal glomerulus are unique cells with a complex cellular organization consisting of a cell body, major processes and foot processes. Podocyte foot processes form a characteristic interdigitating pattern with foot processes of neighboring podocytes, leaving in between the filtration slits that are bridged by the glomerular slit diaphragm. The highly dynamic foot processes contain an actin-based contractile apparatus comparable to that of smooth muscle cells or pericytes. Mutations affecting several podocyte proteins lead to rearrangement of the actin cytoskeleton, disruption of the filtration barrier and subsequent renal disease. The fact that the dynamic regulation of the podocyte cytoskeleton is vital to kidney function has led to podocytes emerging as an excellent model system for studying actin cytoskeleton dynamics in a physiological context.", "Visceral glomerular epithelial cells (GEC) are essential for maintenance of normal glomerular permselectivity. The actin cytoskeleton is a key determinant of GEC morphology and function. In the rat passive Heymann nephritis (PHN) model of membranous nephropathy, complement C5b-9 induces nonlytic GEC injury associated with morphological changes of GEC and proteinuria. The current study addresses the role of Rho family of small GTPases in complement-mediated GEC injury. When cultured rat GEC were stimulated with complement C5b-9 for 18 h, RhoA activity increased, whereas Rac1/Cdc42 activities decreased, compared with control cells. Similar changes in Rho-GTPase activities were observed in glomeruli from rats with PHN. The amount of active p190RhoGAP, a negative upstream regulator of RhoA, was decreased in complement-stimulated GEC, potentially contributing to increased RhoA activity. To address the functional effects of Rho-GTPases, GEC were transfected with constitutively active (CA) or dominant negative (DN) Rho-GTPase mutants. GEC transfected with CA-RhoA showed a smaller and round contour and prominent cortical F-actin. In contrast, GEC transfected with CA-Rac1 demonstrated morphological changes that resembled process formation. In addition, expression of CA-RhoA attenuated complement-mediated cytotoxicity, whereas cytotoxicity was augmented by DN-RhoA. Thus exposure of GEC to complement alters the balance of RhoA, Rac1, and Cdc42 activities. The activity of Rac1 may contribute to process formation, while activation of RhoA (e.g., in the setting of complement attack), with or without blunting of Rac1 activity, may have an opposite effect, i.e., contribute to foot process effacement. Activation of RhoA increases the resistance of GEC to complement-mediated injury.", "Mutations in the NPHS2 gene encoding podocin are implicated in an autosomal-recessive form of nonsyndromic steroid-resistant nephrotic syndrome in both pediatric and adult patients. Patients with homozygous or compound heterozygous mutations commonly present with steroid-resistant nephrotic syndrome before the age of 6 years and rapidly progress to end-stage kidney disease with a very low prevalence of recurrence after renal transplantation. Here, we reviewed all the NPHS2 mutations published between October 1999 and September 2013, and also all novel mutations identified in our personal cohort and in international genetic laboratories. We identified 25 novel pathogenic mutations in addition to the 101 already described. The mutations are distributed along the entire coding region and lead to all kinds of alterations including 53 missense, 17 nonsense, 11 small insertions, 26 small deletions, 16 splicing, two indel mutations, and one mutation in the stop codon. In addition, 43 variants were classified as variants of unknown significance, as these missense changes were exclusively described in the heterozygous state and/or considered benign by prediction software. Genotype-phenotype analyses established correlations between specific variants and age at onset, ethnicity, or clinical evolution. We created a Web database using the Leiden Open Variation Database (www.lovd.nl/NPHS2) software that will allow the inclusion of future reports.", "Synaptopodin is a proline-rich protein intimately associated with actin microfilaments present in the podocytes' foot processes. We investigated for synaptopodin expression in children with idiopathic nephrotic syndrome (INS), including minimal change disease (MCD), diffuse mesangial hypercellularity (DMH), and focal segmental glomerulosclerosis (FSGS); in children with congenital nephrotic syndrome of the Finnish type (CNF); and in normal kidney tissue. In particular, we examined whether an association exists between synaptopodin expression in podocyte cells and the response to steroids in INS, and whether synaptopodin expression can predict FSGS upon the initial kidney biopsy in children who progress from MCD or DMH to FSGS. Immunohistochemistry was performed for synaptopodin expression on renal tissues from MCD (N = 18), DMH (N = 7), FSGS (N = 13), CNF (N = 9), and normal children (N = 7). Synaptopodin expression in nonsclerosed glomeruli was quantitated by computerized image analysis on the Optimastrade mark software for both luminance (L) and percentage of glomerular area (A). Synaptopodin expression was absent in areas of sclerosis. In nonsclerosed glomeruli, synaptopodin was significantly less expressed in all groups of INS and in CNF compared with normal (P < 0.0001 for both L and A, in each MCD, DMH, FSGS, and CNF). In INS, synaptopodin expression decreased in order from MCD to DMH to FSGS, reaching statistical significance between MCD and FSGS (P = 0.001 for L and P = 0.05 for A). Greater synaptopodin expression in podocytes was associated with a significantly better response to steroid therapy (P < 0.05 for both L and A). On the other hand, the expression of synaptopodin did not predict progression of MCD or DMH to FSGS. We conclude that measurement of synaptopodin has the potential to be used as a marker to study the alteration in podocyte cell and response to therapy in INS." ]
Candidate genes associated with in vitro regeneration in cucumber (Cucumis sativus L.)	Candidate genes associated with in vitro regeneration were identified in cucumber. The ability to regenerate shoots or whole plants from differentiated plant tissues is essential for plant transformation. In cucumber (Cucumis sativus L.), regeneration ability varies considerably across accessions, but the genetic mechanism has not yet been demonstrated. In the present study, 148 recombinant inbred lines and a core collection were examined to identify candidate genes involved in cucumber regeneration. Four QTL for cotyledon regeneration that explained 9.7-16.6% of the phenotypic variation in regeneration were identified on cucumber chromosomes 1, 3, and 6. The loci Fcrms1.1 and Fcrms	[ "Most fruits in our daily diet are the products of domestication and breeding. Here we report a map of genome variation for a major fruit that encompasses ~3.6 million variants, generated by deep resequencing of 115 cucumber lines sampled from 3,342 accessions worldwide. Comparative analysis suggests that fruit crops underwent narrower bottlenecks during domestication than grain crops. We identified 112 putative domestication sweeps; 1 of these regions contains a gene involved in the loss of bitterness in fruits, an essential domestication trait of cucumber. We also investigated the genomic basis of divergence among the cultivated populations and discovered a natural genetic variant in a β-carotene hydroxylase gene that could be used to breed cucumbers with enhanced nutritional value. The genomic history of cucumber evolution uncovered here provides the basis for future genomics-enabled breeding.", "Formation of somatic embryos in plants is known to require high concentrations of auxin or 2,4-dichlorophenoxyacetic acid (2,4-D), which presumably acts to trigger a signalling cascade. However, very little is known about the molecular mechanism that mediates the vegetative-to-embryogenic transition. We have employed a genetic approach to dissect the signal transduction pathway during somatic embryogenesis. In a functional screen using a chemical-inducible activation-tagging system, we identified two alleles of Arabidopsis gene PGA6 whose induced overexpression caused high-frequency somatic embryo formation in all tissues and organs tested, without any external plant hormones. Upon inducer withdrawal, all these somatic embryos were able to germinate directly, without any further treatment, and to develop into fertile adult plants. PGA6 was found to be identical to WUSCHEL (WUS), a homeodomain protein previously shown to be involved in specifying stem cell fate in shoot and floral meristems. Transgenic plants carrying an estradiol-inducible XVE-WUS transgene can phenocopy pga6-1 and pga6-2. Our results suggest that WUS/PGA6 also plays a key role during embryogenesis, presumably by promoting the vegetative-to-embryogenic transition and/or maintaining the identity of the embryonic stem cells.", "As more and more genomes are sequenced, genome annotation becomes increasingly important in bridging the gap between sequence and biology. Gene prediction, which is at the center of genome annotation, usually integrates various resources to compute consensus gene structures. However, many newly sequenced genomes have limited resources for gene predictions. In an effort to create high-quality gene models of the cucumber genome (Cucumis sativus var. sativus), based on the EVidenceModeler gene prediction pipeline, we incorporated the massively parallel complementary DNA sequencing (RNA-Seq) reads of 10 cucumber tissues into EVidenceModeler. We applied the new pipeline to the reassembled cucumber genome and included a comparison between our predicted protein-coding gene sets and a published set. The reassembled cucumber genome, annotated with RNA-Seq reads from 10 tissues, has 23, 248 identified protein-coding genes. Compared with the published prediction in 2009, approximately 8, 700 genes reveal structural modifications and 5, 285 genes only appear in the reassembled cucumber genome. All the related results, including genome sequence and annotations, are available at http://cmb.bnu.edu.cn/Cucumis_sativus_v20/. We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes.", "Repeated elements such as satellites and transposons are ubiquitous in eukaryotic genomes. De novo computational identification and classification of such elements is a challenging problem. Therefore, repeat annotation of sequenced genomes has historically largely relied on sequence similarity to hand-curated libraries of known repeat families. We present a new approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster. The PILER software is freely available at http://www.drive5.com/piler.", "We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.", "Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumber's seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and 'fresh green' odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.", "Recent studies have revealed the operation of a long-distance communication network operating within the vascular system of higher plants. The evolutionary development of this network reflects the need to communicate environmental inputs, sensed by mature organs, to meristematic regions of the plant. One consequence of such a long-distance signaling system is that newly forming organs can develop properties optimized for the environment into which they will emerge, mature, and function. The phloem translocation stream of the angiosperms contains, in addition to photosynthate and other small molecules, a variety of macromolecules, including mRNA, small RNA, and proteins. This review highlights recent progress in the characterization of phloem-mediated transport of macromolecules as components of an integrated long-distance signaling network. Attention is focused on the role played by these proteins and RNA species in coordination of developmental programs and the plant's response to both environmental cues and pathogen challenge. Finally, the importance of developing phloem transcriptome and proteomic databases is discussed within the context of advances in plant systems biology." ]
Characteristics and quality of YouTube videos on colorectal cancer	YouTube is the second most visited website in the world. No studies to date have characterized and evaluated YouTube videos on colorectal cancer (CRC) although these videos could influence patient decision-making, notably regarding screening and prevention. This study aims to report the characteristics and quality of these videos as patient education resources for CRC. YouTube's search engine was queried with different search phrases relating to CRC. The first two pages of each search result were analyzed. Two specialists devised a critical appraisal tool with a list of criteria to assess the videos. Quantitative YouTube parameter analyses and criteria assessment were performed. Inter-rater agreement was assessed between three raters. A total of 46 videos were eligible to be included in the study. The videos were on average 4:51 ± 3:27 min long. The videos had 10 times as many likes as dislikes. Less than half the videos discussed risk factors and protective factors. Only 41% of videos mentioned screening tests and only about a quarter discussed them. Palliative care was only mentioned in 2% of videos. A single video could obtain a perfect score on the critical appraisal tool. Length was the unique parameter associated with a high score on the criteria list. There is thus a need for more authoritative and comprehensive videos easily identifiable by the patients. Video popularity is not associated with comprehensiveness. Currently, YouTube might not be an education resource for CRC suited to every patient.	[ "To investigate the content, quality and popularity of information about type 2 diabetes available on YouTube. We searched YouTube with the terms Diabetes, Diabetes type 2, Diabetes South Asians, Diabetes Punjabi and Diabetes Hindi to identify videos concerning type 2 diabetes. A team of health-care providers independently classified the first 20 videos from each search as useful, misleading, or personal experience, rated them on a 5-point global quality scale (GQS) and categorized their content on a 26-point scale in duplicate. Useful videos were rated for reliability by using a 5-point modified DISCERN scale. Higher scores represent better quality, reliability and comprehensiveness. Of 100 videos, 71 met the inclusion criteria; 45 (63.4%) were rated as useful (median GQS, 3; interquartile range [IQR], 2 to 4); and 23 (32.4%) were deemed misleading (median GQS, 1; IQR, 1 to 2). Median reliability and content scores for useful videos were 3 (IQR, 2 to 3) and 5 (IQR, 3 to 10), respectively, and 6 videos met ≥ 4 of 5 reliability criteria. Overall, misleading videos were more popular than useful videos (median, 233 views/day; IQR, 26 to 523; vs. 8.3 views/day; IQR, 0.4 to 134.6; p<0.01). Culturally tailored videos were just as likely to be misleading and had similar GQS scores in comparison to nonculturally tailored videos (32.1% vs. 32.6% and 3 vs. 3, respectively). The quality of identified videos concerning type 2 diabetes was variable, and misleading videos were popular. Further creation and curation of high-quality video resources is required.", "To assess the quality of the content of YouTube videos for cataract surgery patient education. Hotel Dieu Hospital, Kingston, Ontario, Canada. Observational study. \"Cataract surgery,\" \"cataract surgery for patients,\" and \"cataract surgery patient education\" were used as search terms. The first two pages of search results were reviewed. Descriptive statistics such as video length and view count were obtained. Two cataract surgeons devised 14 criteria important for educating patients about the procedure. Videos were analyzed based on the presence or absence of these criteria. Videos were also assessed for whether they had a primary commercial intent. Seventy-two videos were analyzed after excluding 48 videos that were duplicate, irrelevant, or not in English. The majority of videos came from a medical professional (71%) and many depicted a real cataract surgery procedure (43%). Twenty-one percent of the videos had a primary commercial intent to promote a practice or product. Out of a total possible 14 points, the mean number of usefulness criteria satisfied was only 2.28 ± 1.80. There was no significant difference in view count between the most useful videos and other videos (p = 0.94). Videos from medical organizations such as the National Health Service were more useful (p < 0.0001). Cataract surgery videos are popular on YouTube, but most are not adequately educational. Patients may be receiving biased information from videos created with primary commercial intent. Physicians should be aware of the type of information patients may be accessing on YouTube.", "The widespread prevalence and persistence of misinformation in contemporary societies, such as the false belief that there is a link between childhood vaccinations and autism, is a matter of public concern. For example, the myths surrounding vaccinations, which prompted some parents to withhold immunization from their children, have led to a marked increase in vaccine-preventable disease, as well as unnecessary public expenditure on research and public-information campaigns aimed at rectifying the situation. We first examine the mechanisms by which such misinformation is disseminated in society, both inadvertently and purposely. Misinformation can originate from rumors but also from works of fiction, governments and politicians, and vested interests. Moreover, changes in the media landscape, including the arrival of the Internet, have fundamentally influenced the ways in which information is communicated and misinformation is spread. We next move to misinformation at the level of the individual, and review the cognitive factors that often render misinformation resistant to correction. We consider how people assess the truth of statements and what makes people believe certain things but not others. We look at people's memory for misinformation and answer the questions of why retractions of misinformation are so ineffective in memory updating and why efforts to retract misinformation can even backfire and, ironically, increase misbelief. Though ideology and personal worldviews can be major obstacles for debiasing, there nonetheless are a number of effective techniques for reducing the impact of misinformation, and we pay special attention to these factors that aid in debiasing. We conclude by providing specific recommendations for the debunking of misinformation. These recommendations pertain to the ways in which corrections should be designed, structured, and applied in order to maximize their impact. Grounded in cognitive psychological theory, these recommendations may help practitioners-including journalists, health professionals, educators, and science communicators-design effective misinformation retractions, educational tools, and public-information campaigns.", "Colorectal cancer screening rates have increased significantly in Kentucky, from 35% in 1999 to 66% in 2012. A continued improvement in screening requires identification of existing barriers and implementation of interventions to address barriers. The state of Kentucky added a question to the 2012 Kentucky Behavioral Risk Factor Surveillance System survey for respondents aged 50 years or older who answered no to ever having been screened for colorectal cancer by colonoscopy or sigmoidoscopy to assess the reasons why respondents had not been screened. Combined responses constituted 4 categories: attitudes and beliefs, health care provider and health care systems barriers, cost, and other. Prevalence estimates for barriers were calculated by using raking weights and were stratified by race/ethnicity, sex, education, income, and health insurance coverage. Logistic regression estimated odds ratios for barriers to screening. The most common barriers in all areas were related to attitudes and beliefs, followed by health care provider and systems, and cost. Non-Hispanic whites and respondents with more than a high school education were more likely to choose attitudes and beliefs as a barrier than were non-Hispanic blacks and those with less than a high school education. Respondents with low incomes and with no insurance were significantly more likely to select cost as a barrier. No significant associations were observed between demographic variables and the selection of a health care provider and a health care system. Barriers related to education, race/ethnicity, income, and insurance coverage should be considered when designing interventions. Expansion of Medicaid and implementation of the Affordable Care Act in Kentucky could have an impact on reducing these barriers.", "Patient education materials should be written at a level that is understandable for patients with low health literacy. The aims of this study are (1) to review the literature on readability of ophthalmic patient education materials and (2) to evaluate and revise our institution's patient education materials about glaucoma using evidence-based guidelines on writing for patients with low health literacy. A systematic search was conducted on the PubMed/MEDLINE database for studies that have evaluated readability level of ophthalmic patient education materials, and the reported readability scores were assessed. Additionally, we collected evidence-based guidelines for writing easy-to-read patient education materials, and these recommendations were applied to revise 12 patient education handouts on various glaucoma topics at our institution. Readability measures, including Flesch-Kincaid Grade Level (FKGL), and word count were calculated for the original and revised documents. The original and revised versions of the handouts were then scored in random order by two glaucoma specialists using the Suitability Assessment of Materials (SAM) instrument, a grading scale used to evaluate suitability of health information materials for patients. Paired t test was used to analyze changes in readability measures, word count, and SAM score between original and revised handouts. Finally, five glaucoma patients were interviewed to discuss the revised materials, and patient feedback was analyzed qualitatively. Our literature search included 13 studies that evaluated a total of 950 educational materials. Among the mean FKGL readability scores reported in these studies, the median was 11 (representing an eleventh-grade reading level). At our institution, handouts' readability averaged a tenth-grade reading level (FKGL = 10.0 ± 1.6), but revising the handouts improved their readability to a sixth-grade reading level (FKGL = 6.4 ± 1.2) (p < 0.001). Additionally, the mean SAM score of our institution's handouts improved from 60 ± 7 % (adequate) for the original versions to 88 ± 4 % (superior) for the revised handouts (p < 0.001). Our systematic review of the literature reveals that ophthalmic patient education materials are consistently written at a level that is too high for many patients to understand. Our institution's experience suggests that applying guidelines on writing easy-to-understand material can improve the readability and suitability of educational materials for patients with low health literacy.", "Decision aids are now a well-established means of supporting patients in their medical decision making. The widespread use of decision aids invites questions about how their components contribute to patient decisions. The objective of this study was to measure the importance of second opinions, patient-specific outcome forecasts, and patient testimonials relative to patient clinical and socioeconomic factors and the primary physician recommendation on the decision to undergo full knee replacement surgery to treat knee osteoarthritis. Middle-aged and older members of the RAND American Life Panel (N = 1616) chose whether to recommend surgery as a treatment for each of 3 hypothetical patients (vignettes) presented in a video-enhanced internet survey. Vignettes randomly sampled levels of scenario attributes. Second opinions, person-specific outcome forecasts, and 2 consistent patient testimonials strongly affected respondents' decision making; a single testimonial, however, did not significantly affect decisions. Information provided in a decision aid, including person-specific outcome forecasts and testimonials, can affect patient choices. The strong effect of testimonials and respondents' interest in reviewing them reinforces concerns about unwanted influence when testimonials are biased." ]
Treatment of progressive multiple sclerosis	Despite the fact that majority of patients with multiple sclerosis (MS) have relapsing-remitting disease, many transition to secondary progressive disease (SPMS) over time. This transition is thought to be related to neurodegenerative processes increasingly predominating over inflammatory processes as the driving forces of disability. However, some patients initially present with primary progressive disease (PPMS) that is characterized by a gradual accumulation of neurological symptoms and subsequent disability accumulation. The treatment of both PPMS and SPMS, collectively referred to as progressive MS, has proven quite challenging due to the multifactorial and poorly understood pathophysiology of multiple sclerosis in general, specifically that of progressive disease. The purpose of this article is to discuss important clinical and pathophysiologic differences between relapsing and progressive forms of MS, review previous notable trials of drugs in progressive MS, examine current literature regarding recent and promising progressive MS treatments, and discuss future considerations for progressive MS therapeutics and management. Specifically, the current evidence regarding treatment of progressive MS with ocrelizumab, simvastatin, ibudilast, alpha-lipoic acid, high-dose biotin, siponimod, and cell-based therapies are discussed.	[ "Multiple sclerosis (MS), an inflammatory demyelinating disease, is a major cause of neurological disability in young adults in the developed world. Although the progressive neurological disability that most patients with MS eventually experience results from axonal degeneration, little is known about the mechanisms of axonal injury in MS. Accumulating evidence suggests that the increased energy demand of impulse conduction along excitable demyelinated axons and reduced axonal ATP production induce a chronic state of virtual hypoxia in chronically demyelinated axons. In response to such a state, key alterations that contribute to chronic necrosis of axons might include mitochondrial dysfunction (due to defective oxidative phosphorylation or nitric oxide production), Na+ influx through voltage-gated Na+ channels and axonal AMPA receptors, release of toxic Ca2+ from the axoplasmic reticulum, overactivation of ionotropic and metabotropic axonal glutamate receptors, and activation of voltage-gated Ca2+ channels, ultimately leading to excessive stimulation of Ca2+-dependent degradative pathways. The development of neuroprotective therapies that target these mechanisms might constitute effective adjuncts to currently used immune-modifying agents.", "Vaccination with self peptides contained within T cell receptor (TCR) chains, expressed by pathogenic Th1 cells can induce a second set of regulatory T cells that can reverse paralysis in rodents with experimental encephalomyelitis, and similarly, may have the potential to regulate myelin-reactive Th1 cells in patients with multiple sclerosis (MS). In this review, we discuss our recent discovery that TCR-reactive T cells generally possess classical inhibitory activity associated with Treg cells. CD4+CD25+ TCR-reactive T cells can inhibit CD4+CD25- indicator cells stimulated with anti-CD3/anti-CD28 antibody in a dose-dependent and cell-contact-dependent manner. Additionally, CD4+CD25+ T cells from blood of healthy control donors have significant responses to a pool of discriminatory TCR peptides, including BV10S1P, BV19S20, BV13S7, BV12S2A2T, BV11S1A1T, BV21S3A1T, AV15S1, and BV12S1A1N1. Patients with MS have varying degrees of deficient responses to TCR peptides, and by association, a defect in Treg cell function as well. TCR peptide vaccination using a new tripeptide mixture emulsified in IFA produced strong T cell responses in 100% of MS recipients, a dramatic improvement over previous vaccines given i.d. in saline that induced TCR-reactive T cell responses in about 50% of recipients. Responders to vaccination had a tendency towards reduced MRI lesions, and an early indication of enhanced Treg activity mediated by TCR-reactive T cells that could provide suppression of target as well as bystander T cells. These data provide a strong foundation for future TCR vaccination studies that will critically test the ability of the tripeptide mixture to induce significantly enhanced Treg activity and possible clinical and MRI benefits in vivo.", "More than half of patients with multiple sclerosis have progressive disease characterised by accumulating disability. The absence of treatments for progressive multiple sclerosis represents a major unmet clinical need. On the basis of evidence that mesenchymal stem cells have a beneficial effect in acute and chronic animal models of multiple sclerosis, we aimed to assess the safety and efficacy of these cells as a potential neuroprotective treatment for secondary progressive multiple sclerosis. Patients with secondary progressive multiple sclerosis involving the visual pathways (expanded disability status score 5·5-6·5) were recruited from the East Anglia and north London regions of the UK. Participants received intravenous infusion of autologous bone-marrow-derived mesenchymal stem cells in this open-label study. Our primary objective was to assess feasibility and safety; we compared adverse events from up to 20 months before treatment until up to 10 months after the infusion. As a secondary objective, we chose efficacy outcomes to assess the anterior visual pathway as a model of wider disease. Masked endpoint analyses was used for electrophysiological and selected imaging outcomes. We used piecewise linear mixed models to assess the change in gradients over time at the point of intervention. This trial is registered with ClinicalTrials.gov, number NCT00395200. We isolated, expanded, characterised, and administered mesenchymal stem cells in ten patients. The mean dose was 1·6×10(6) cells per kg bodyweight (range 1·1-2·0). One patient developed a transient rash shortly after treatment; two patients had self-limiting bacterial infections 3-4 weeks after treatment. We did not identify any serious adverse events. We noted improvement after treatment in visual acuity (difference in monthly rates of change -0·02 logMAR units, 95% CI -0·03 to -0·01; p=0·003) and visual evoked response latency (-1·33 ms, -2·44 to -0·21; p=0·020), with an increase in optic nerve area (difference in monthly rates of change 0·13 mm(2), 0·04 to 0·22; p=0·006). We did not identify any significant effects on colour vision, visual fields, macular volume, retinal nerve fibre layer thickness, or optic nerve magnetisation transfer ratio. Autologous mesenchymal stem cells were safely given to patients with secondary progressive multiple sclerosis in our study. The evidence of structural, functional, and physiological improvement after treatment in some visual endpoints is suggestive of neuroprotection. Medical Research Council, Multiple Sclerosis Society of Great Britain and Northern Ireland, Evelyn Trust, NHS National Institute for Health Research, Cambridge and UCLH Biomedical Research Centres, Wellcome Trust, Raymond and Beverly Sackler Foundation, and Sir David and Isobel Walker Trust.", "Leptomeningeal inflammation is associated with increased cortical damage and worse clinical outcomes in MS. It may be detected on contrast-enhanced T2-FLAIR imaging as focal leptomeningeal contrast-enhancement (LME). To assess the safety of intrathecal (IT) rituximab in progressive MS (PMS) and to assess its effects on LME and CSF biomarkers. PMS patients had a screening MRI to detect LME. Participants satisfying eligibility criteria underwent two IT administrations of 25 mg rituximab 2 weeks apart. Follow-up lumbar puncture and MRI were performed at 8 and 24 weeks after the first treatment. Of 36 patients screened 15 had LME, 11 consented, and 8 received study treatment. Mean age was 56.7 years and number of LME lesions ranged from 1 to 3. No serious adverse effects occurred. We noted profound reductions in peripheral B cells from baseline to week 2 and 8 with some return at week 24. We also observed transient reductions in CSF B cells and CXCL-13 levels with an increase in BAFF levels. However, the number of LME did not change following treatment. IT rituximab was well tolerated in PMS patients and had transient effects on CSF biomarkers but did not change LME.", "A limited amount of data exists regarding the effect of lipoic acid (LA), an oral antioxidant supplement, on cytokine profiles among multiple sclerosis (MS) patients. We aimed to assess the effect of daily consumption of LA on the cytokine profiles in MS patients. In this double-blind, placebo-controlled, randomized clinical trial, 52 relapsing-remitting MS patients with an age range of 18-50 years were recruited into 2 groups: LA consumption (1,200 mg/day) or placebo. Patients followed their prescribed supplements for 12 weeks. Fasting blood samples for cytokine profile measurement were collected at baseline and after the intervention. Anthropometric parameters were measured based on the standard guidelines. INF-γ, ICAM-1, TGF-β and IL-4 were significantly reduced in the LA group compared to the placebo group [(INF-γ: 0.82 ± 0.2 vs. 0.2 ± 0.2 pg/ml, p < 0.0001), (ICAM-1: 20.2 ± 9.4 vs. 8 ± 10 ng/ml, p = 0.0001), (TGF-β: 103.1 ± 20.2 vs. 54.9 ± 26 ng/ml, p < 0.0001) and (IL-4: 0.1 ± 0.1 vs. 1.02 ± 1.7 ng/ml, p = 0.0112)]. No significant changes in TNF-α, IL-6, EDSS and MMP-9 were found between the LA and placebo groups (p = 0.6, p = 0.8, p = 0.09 and p = 0.8, respectively). The results suggested that consumption of 1,200 mg LA per day beneficially affects several inflammatory cytokines including INF-γ, ICAM-1 TGF-β and IL-4. Further investigations are needed to verify the beneficial role of LA on other cytokine profiles among MS patients.", "Alpha-lipoic acid (alpha-LA) is a neuroprotective metabolic antioxidant that has been shown to cross the blood brain barrier. We tested whether alpha-LA is capable to prevent MOG35-55-induced experimental autoimmune encephalomyelitis (EAE), an established model of multiple sclerosis (MS). Daily oral administration of alpha-LA, starting at the time of immunization, significantly prevented EAE progression as compared to control mice. This was associated with a reduction of CNS infiltrating T cells and macrophages as well as decreased demyelination. We then tested alpha-LA in a therapeutic protocol aimed at suppressing EAE after its onset. Intraperitoneal (i.p.), but not oral, administration of alpha-LA significantly prevented disease progression when compared to vehicle-treated controls. Similarly, we observed significant reduction of demyelination and inflammatory infiltration. This clinical effect was not due to an impairment of MOG35-55 recognition by encephalitogenic T cells. In contrast, MOG-specific T cells showed a decreased production of IFNgamma and IL-4, suggesting an immunosuppressive activity on both Th1 and Th2 cytokines. In addition, alpha-LA inhibited the proteolytic activity of MMP2 and MMP9 only at very high doses. Our data indicate that alpha-LA can effectively interfere with the autoimmune reaction associated with EAE through mechanisms other than its antioxidant activity and supports further studies on the use of alpha-LA as a potential therapy for MS.", "Mesenchymal stem cells (MSCs) are pluripotent non-hematopoietic precursor cells that can be isolated from bone marrow and numerous other tissues, culture-expanded to purity, and induced to differentiate in vitro and in vivo into mesodermal derivatives. MSCs exhibit many phenotypic and functional similarities to pericytes. The immunomodulatory, tissue protective, and repair-promoting properties of MSCs demonstrated both in vitro and in animal models make them an attractive potential therapy for MS and other conditions characterized by inflammation and/or tissue injury. Other potential advantages of MSCs as a therapeutic include the relative ease of culture expansion, relative immunoprivilege allowing allogeneic transplantation, and their ability to traffic from blood to areas of tissue allowing intravascular administration. The overall published experience with MSC transplantation in MS is modest, but several small case series and preliminary studies yielded promising results. Several groups, including us, recently initiated formal studies of autologous, culture-expanded, bone marrow-derived MSC transplantation in MS. Although there are several potential safety concerns, to date, the procedure has been well tolerated. Future studies that more definitively assess efficacy also will need to address several technical issues.", "Partial blockade of voltage-gated sodium channels is neuroprotective in experimental models of inflammatory demyelinating disease. In this phase 2 trial, we aimed to assess whether the sodium-channel blocker lamotrigine is also neuroprotective in patients with secondary progressive multiple sclerosis. Patients with secondary progressive multiple sclerosis who attended the National Hospital for Neurology and Neurosurgery or the Royal Free Hospital, London, UK, were eligible for inclusion in this double-blind, parallel-group trial. Patients were randomly assigned via a website by minimisation to receive lamotrigine (target dose 400 mg/day) or placebo for 2 years. Treating physicians, evaluating physicians, and patients were masked to treatment allocation. The primary outcome was the rate of change of partial (central) cerebral volume over 24 months. All patients who were randomly assigned were included in the primary analysis. This trial is registered with ClinicalTrials.gov, NCT00257855. 120 patients were randomly assigned to treatment (87 women and 33 men): 61 to lamotrigine and 59 to placebo. 108 patients were analysed for the primary endpoint: 52 in the lamotrigine group and 56 in the placebo group. The mean change in partial (central) cerebral volume per year was -3.18 mL (SD -1.25) in the lamotrigine group and -2.48 mL (-0.97) in the placebo group (difference -0.71 mL, 95% CI -2.56 to 1.15; p=0.40). However, in an exploratory modelling analysis, lamotrigine treatment seemed to be associated with greater partial (central) cerebral volume loss than was placebo in the first year (p=0.04), and volume increased partially after treatment stopped (p=0.04). Lamotrigine treatment reduced the deterioration of the timed 25-foot walk (p=0.02) but did not affect other secondary clinical outcome measures. Rash and dose-related deterioration of gait and balance were experienced more by patients in the lamotrigine group than the placebo group. The effect of lamotrigine on cerebral volume of patients with secondary progressive multiple sclerosis did not differ from that of placebo over 24 months, but lamotrigine seemed to cause early volume loss that reversed partially on discontinuation of treatment. Future trials of neuroprotection in multiple sclerosis should include investigation of complex early volume changes in different compartments of the CNS, effects unrelated to neurodegeneration, and targeting of earlier and more inflammatory disease. Multiple Sclerosis Society of Great Britain and Northern Ireland.", "Rituximab, a monoclonal antibody selectively depleting CD20+ B cells, has demonstrated efficacy in reducing disease activity in relapsing-remitting multiple sclerosis (MS). We evaluated rituximab in adults with primary progressive MS (PPMS) through 96 weeks and safety through 122 weeks. Using 2:1 randomization, 439 PPMS patients received two 1,000 mg intravenous rituximab or placebo infusions every 24 weeks, through 96 weeks (4 courses). The primary endpoint was time to confirmed disease progression (CDP), a prespecified increase in Expanded Disability Status Scale sustained for 12 weeks. Secondary endpoints were change from baseline to week 96 in T2 lesion volume and total brain volume on magnetic resonance imaging scans. Differences in time to CDP between rituximab and placebo did not reach significance (96-week rates: 38.5% placebo, 30.2% rituximab; p = 0.14). From baseline to week 96, rituximab patients had less (p < 0.001) increase in T2 lesion volume; brain volume change was similar (p = 0.62) to placebo. Subgroup analysis showed time to CDP was delayed in rituximab-treated patients aged <51 years (hazard ratio [HR] = 0.52; p = 0.010), those with gadolinium-enhancing lesions (HR = 0.41; p = 0.007), and those aged <51 years with gadolinium-enhancing lesions (HR = 0.33; p = 0.009) compared with placebo. Adverse events were comparable between groups; 16.1% of rituximab and 13.6% of placebo patients reported serious events. Serious infections occurred in 4.5% of rituximab and <1.0% of placebo patients. Infusion-related events, predominantly mild to moderate, were more common with rituximab during the first course, and decreased to rates comparable to placebo on successive courses. Although time to CDP between groups was not significant, overall subgroup analyses suggest selective B-cell depletion may affect disease progression in younger patients, particularly those with inflammatory lesions.", "Statins have been prescribed extensively for their cholesterol-lowering properties and efficacy in cardiovascular disease. However, compelling evidence now exists that statins also have extensive immunomodulatory properties that operate independently of lipid lowering. Consequently, much attention has been directed towards their potential as therapeutic agents for the treatment of autoimmune disease. Modulation of post-translational protein prenylation seems to be a key mechanism by which statins alter immune function. In this Review, the effect of statin therapy on immune function, and how this relates to the pathogenesis of autoimmune disease, is reviewed alongside current opinion of what the key biological targets of statins are." ]
The Extracellular Matrix in Autoimmune Type 1 Diabetes	There is a growing appreciation that the extracellular matrix (ECM) contributes to both the maintenance of immune tolerance in healthy tissues and to its loss at sites of autoimmunity. Here, we review recent literature on the role of ECM and particularly the glycosaminoglycans hyaluronan and heparan sulfate in the development of autoimmune, type 1 diabetes (T1D). Data from transplant models suggest that healthy islets are embedded within an intact ECM that supports beta-cell homeostasis and provides physical and immunoregulatory barriers against immune infiltration. However, studies of human insulitis as well as the non-obese diabetic (NOD) and DORmO mouse models of T1D indicate that autoimmune insulitis is associated with the degradation of basement membrane structures, the catabolism of the islet interstitium, and the accumulation of a hyaluronan-rich, pro-inflammatory ECM. Moreover, in these models of autoimmune diabetes, either the pharmacologic inhibition of heparan sulfate catabolism, the reduction of hyaluronan synthesis, or the targeting of the pathways that sense these ECM changes can all prevent beta-cell destruction. Together these data support an emerging paradigm that in healthy islets the local ECM contributes to both immune tolerance and beta-cell homeostasis while in chronic inflammation the islet ECM is permissive to immune infiltration and beta-cell destruction. Therapies that support ECM-mediated 'barrier tolerance' may have potential as adjunctive agents in combination regimens designed to prevent or treat autoimmunity.	[ "CD4(+)Foxp3(+) regulatory T (T reg) cells play an essential role in maintaining immunological tolerance via their suppressive function on conventional CD4(+) T (Tconv) cells. Repertoire studies suggest that distinct T cell receptor signaling pathways lead to T reg differentiation, but the signals that regulate T reg specification are largely unknown. We identify AKT as a strong repressor of entry into the T reg phenotype in vitro and in vivo. A constitutively active allele of AKT substantially diminished TGF-beta-induced Foxp3 expression in a kinase-dependent manner and via a rapamycin-sensitive pathway, implicating the AKT-mammalian target of rapamycin axis. The observed impairment in Foxp3 induction was part of a broad dampening of the typical T reg transcriptional signature. Expression of active AKT at a stage before Foxp3 turn on during normal T reg differentiation in the thymus selectively impaired differentiation of CD4(+)Foxp3(+) cells without any alteration in the positive selection of Tconv. Activated AKT, in contrast, did not affect established Foxp3 expression in T reg cells. These results place AKT at a nexus of signaling pathways whose proper activation has a strong and broad impact on the onset of T reg specification.", "CD4(+) effector T cells have been categorized into two subsets: T helper type 1 (T(H)1) and T(H)2. Another subset of T cells that produce interleukin 17 (IL-17; 'T(H)-17 cells') has been identified that is highly proinflammatory and induces severe autoimmunity. Whereas IL-23 serves to expand previously differentiated T(H)-17 cell populations, IL-6 and transforming growth factor-beta (TGF-beta) induce the differentiation of T(H)-17 cells from naive precursors. These data suggest a dichotomy between CD4(+) regulatory T cells positive for the transcription factor Foxp3 and T(H)-17 cells: TGF-beta induces Foxp3 and generates induced regulatory T cells, whereas IL-6 inhibits TGF-beta-driven Foxp3 expression and together with TGF-beta induces T(H)-17 cells. Emerging data regarding T(H)-17 cells suggest a very important function for this T cell subset in immunity and disease.", "The histologic hallmark of the development of type 1 diabetes (T1D) is insulitis, characterized by leukocytic infiltration of the pancreatic islets. The molecules controlling the early influx of leukocytes into the islets are poorly understood. Tumor necrosis factor alpha (TNFalpha)-stimulated gene 6 (TSG-6) is involved in inflammation, extracellular matrix formation, cell migration, and development. In the present study, we examined the expression and cellular localization of TSG-6 protein in islets of female non-obese diabetic (NOD) mice using frozen section immunofluorescence staining. Pancreata from nondiabetic (8 and 25 weeks old), prediabetic (230-280 mg/dl blood glucose) and diabetic (>300 mg/dl blood glucose) NOD mice were stained for TSG-6, insulin, CD3, CD11c, Mac3 and CD31. TSG-6 protein was detected in 67% of islets of prediabetic mice, 27% of islets of 25-week old nondiabetic mice, and less than 7% of islets of diabetic mice and 8-week old nondiabetic mice. Lastly, islet-derived TSG-6 protein was localized to the infiltrating CD3 and CD11c positive leukocytes.", "The tissue microenvironment contributes to local immunity and to the pathogenesis of autoimmune diseases - a diverse set of conditions characterized by sterile inflammation, immunity against self-antigens, and destruction of tissues. However, the specific factors within the tissue microenvironment that contribute to local immune dysregulation in autoimmunity are poorly understood. One particular tissue component implicated in multiple autoimmune diseases is hyaluronan (HA), an extracellular matrix (ECM) polymer. HA is abundant in settings of chronic inflammation and contributes to lymphocyte activation, polarization, and migration. Here, we first describe what is known about the size, amount, and distribution of HA at sites of autoimmunity and in associated lymphoid structures in type 1 diabetes, multiple sclerosis, and rheumatoid arthritis. Next, we examine the recent literature on HA and its impact on adaptive immunity, particularly in regards to the biology of lymphocytes and Foxp3+ regulatory T-cells (Treg), a T-cell subset that maintains immune tolerance in healthy individuals. We propose that HA accumulation at sites of chronic inflammation creates a permissive environment for autoimmunity, characterized by CD44-mediated inhibition of Treg expansion. Finally, we address potential tools and strategies for targeting HA and its receptor CD44 in chronic inflammation and autoimmunity.", "The mechanisms that regulate basal T cell size and metabolic activity are uncertain. Since the phosphatidylinositol-3 phosphate kinase (PI3 K) and Akt (PKB) pathway has been shown in model organisms to regulate both cell size and metabolism, we generated transgenic mice expressing a constitutively active form of Akt (myristoylated Akt, mAkt) in T cells. Naive transgenic T cells were enlarged and had increased rates of glycolysis compared to control T cells. In addition, mAkt transgenic T cells resisted death-by-neglect upon in vitro culture. Upon activation, mAkt-transgenic T cells were less dependent than control cells on costimulation through CD28 and could both grow rapidly and secrete cytokines in the absence of CD28 ligation. In addition, transgenic expression of mAkt led to the accumulation of CD4 T cells and B cells with age. Many aged mAkt-transgenic mice also developed autoimmunity with immunoglobulin deposits on kidney glomeruli and displayed increased incidence of lymphoma. Together, these data show that Akt activation is sufficient to increase basal T cell size and metabolism. Enhancement of T cell metabolism by Akt and more rapid CD28-independent T cell growth may contribute to the accumulation of excess immune cells and the development of lymphoma and autoimmunity.", "In this experiment, various conditions for embedding cultures of human pancreatic islets in type I collagen gel were studied in an attempt to maintain the highly differentiated functions of islet cells and particularly insulin secretion over a long period of time. The islets isolated by a collagenase digestion technique were plated either on or within the collagen gel and refed with either Eagle's minimum essential medium (5.5 mM D-glucose) or RPMI 1640 medium (11 mM D-glucose) supplemented with 10% FCS and antibiotics. The comparison between the two culture media showed that embedded islets cultured in RPMI had a higher basal insulin secretion rate, survived longer than their MEM counterparts, but exhibited impaired response to an acute glucose test contrasting thus with islets cultured in MEM. The secretory behaviour of islets was also related to the different morphological modifications occurring during culture. Islets directly embedded within the collagen gel more or less maintained their spherical structure and highest secretory capacities. When overlaid with a second layer of collagen, well established monolayers of human islet cells grown on collagen underwent a gradual and complete reorganization into a three-dimensional islet-like structure with a striking reinforcement of their secretory activity. Both cultures were able to survive more than 8 weeks, thus proving the usefulness of such a new model for long-term culture. In contrast, standard cultures on culture treated plastic dishes on which islets cells rapidly established wide monolayers, exhibited a rapid and definitive decline in insulin secretion with a survival not exceeding 14 days. In the light of these different culture conditions, possible mechanisms responsible for disturbance of hormonal release and their implications for in-vitro study of isolated islets functions are discussed. In conclusion, this work is a new example of the permissive effects of collagen matrices on the establishment or maintenance of tissue-like structures in vitro, suggesting the definition of a new model for the study of human pancreatic islets in long-term culture.", "Human islet expansion in monolayer culture leads to loss of function and senescence. By maintaining the 3-D configuration of islets in fibrin gels, it is feasible to expand beta-cells in response to hepatocyte growth factor (HGF) while preserving physiologic glucose responsiveness both in vitro and in vivo after transplantation into nude mice. Islets were cultured free floating with or without growth factors and nicotinamide and in fibrin gels with the same conditions. Proliferation was observed only in islets cultured in fibrin gels and the cocktail; total insulin increased by threefold, with a concomitant increase in beta-cell mass by morphometry. Insulin release after glucose challenge was also preserved. Islets in fibrin gels gave rise in vivo to large grafts rich in insulin and glucagon, and grafts from free-floating islets were smaller with fewer endocrine cells. Circulating human C-peptide levels were higher than in the mice receiving free-floating islets. In summary, fibrin allows for HGF-mediated cell proliferation while preserving glucose responsiveness in an environment that preserves cell-cell contacts. Limited islet ex vivo expansion under these conditions may improve recipient-donor tissue ratios to equal the functional results of whole-organ transplants." ]
Characterization of Thymus-Dependent and Thymus-Independent Immunoglobulin Isotype Responses in Mice Using Enzyme-Linked Immunosorbent Assay	Antibodies, also termed as immunoglobulins (Ig), secreted by differentiated B lymphocytes, plasmablasts/plasma cells, in humoral immunity provide a formidable defense against invading pathogens via diverse mechanisms. One major goal of vaccination is to induce protective antigen-specific antibodies to prevent life-threatening infections. Both thymus-dependent (TD) and thymus-independent (TI) antigens can elicit robust antigen-specific IgM responses and can also induce the production of isotype-switched antibodies (IgG, IgA and IgE) as well as the generation of memory B cells with the help provided by antigen presenting cells (APCs). Here, we describe a protocol to characterize TD and TI Ig isotype responses in mice using enzyme-linked immunosorbent assay (ELISA). In this protocol, TD and TI Ig responses are elicited in mice by intraperitoneal (i.p.) immunization with hapten-conjugated model antigens TNP-KLH (in alum) and TNP-polysaccharide (in PBS), respectively. To induce TD memory response, a booster immunization of TNP-KLH in alum is given at 3 weeks after the first immunization with the same antigen/adjuvant. Mouse sera are harvested at different time points before and after immunization. Total serum Ig levels and TNP-specific antibodies are subsequently quantified using Ig isotype-specific Sandwich and indirect ELISA, respectively. In order to correctly quantify the serum concentration of each Ig isotype, the samples need to be appropriately diluted to fit within the linear range of the standard curves. Using this protocol, we have consistently obtained reliable results with high specificity and sensitivity. When used in combination with other complementary methods such as flow cytometry, in vitro culture of splenic B cells and immunohistochemical staining (IHC), this protocol will allow researchers to gain a comprehensive understanding of antibody responses in a given experimental setting.	[ "The oncogenic EBV protein LMP1 mimics a dysregulated CD40 receptor in vitro. To compare CD40 and LMP1-mediated events in vivo, transgenic mice were engineered to express mouse CD40 (mCD40tg) or a protein with extracellular mCD40 and cytoplasmic LMP1 (mCD40-LMP1tg). Transgenic and CD40(-/-) mice were bred so that only the transgenic CD40 molecule is expressed in B cells, macrophages, and dendritic cells. mCD40-LMP1tg mice had normal lymphocyte subsets, and immunization elicited an antibody response featuring normal isotype switching, affinity maturation, and germinal center (GC) formation. However, unimmunized mCD40-LMP1tg mice had expanded immature and germinal center B cells, produced autoantibodies, exhibited marked splenomegaly and lymphadenopathy, and elevated serum IL-6. Thus, signaling through the LMP1 cytoplasmic tail results in amplified and abnormal mimicry of CD40 functions in vivo, indicating possible ways in which LMP1 contributes to the pathogenesis of EBV-associated human disease.", "Tumor necrosis factor receptor-associated factor 3 (TRAF3) is an adaptor protein that directly binds to a number of receptors of the tumor necrosis factor receptor (TNF-R) superfamily. Despite in vitro evidence that TRAF3 plays diverse roles in different cell types, little is known about the in vivo functions of TRAF3. To address this gap in knowledge and to circumvent the early lethal effect of TRAF3 null mutations, we generated conditional TRAF3-deficient mice. B-cell-specific Traf3(-/-) mice displayed severe peripheral B cell hyperplasia, which culminated in hyperimmunoglobulinemia and increased T-independent antibody responses, splenomegaly and lymphadenopathy. Resting splenic B cells from these mice exhibited remarkably prolonged survival ex vivo independent of B cell activating factor and showed increased amounts of active nuclear factor-kappaB2 but decreased amounts of nuclear protein kinase Cdelta. Furthermore, these mice developed autoimmune manifestations as they aged. These findings indicate that TRAF3 is a critical regulator of peripheral B cell homeostasis and may be implicated in the regulation of peripheral self-tolerance induction.", "Vaccines are the most effective and cost-efficient method for preventing diseases caused by infectious pathogens. Despite the great success of vaccines, development of safe and strong vaccines is still required for emerging new pathogens, re-emerging old pathogens, and in order to improve the inadequate protection conferred by existing vaccines. One of the most important strategies for the development of effective new vaccines is the selection and usage of a suitable adjuvant. Immunologic adjuvants are essential for enhancing vaccine potency by improvement of the humoral and/or cell-mediated immune response to vaccine antigens. Thus, formulation of vaccines with appropriate adjuvants is an attractive approach towards eliciting protective and long-lasting immunity in humans. However, only a limited number of adjuvants is licensed for human vaccines due to concerns about safety and toxicity. We summarize current knowledge about the potential benefits of adjuvants, the characteristics of adjuvants and the mechanisms of adjuvants in human vaccines. Adjuvants have diverse modes of action and should be selected for use on the basis of the type of immune response that is desired for a particular vaccine. Better understanding of current adjuvants will help exploring new adjuvant formulations and facilitate rational design of vaccines against infectious diseases.", "This review presents an overview of the current knowledge of TRAF molecules in inflammation with an emphasis on available human evidence and direct in vivo evidence of mouse models that demonstrate the contribution of TRAF molecules in the pathogenesis of inflammatory diseases. The tumor necrosis factor receptor (TNF-R)-associated factor (TRAF) family of cytoplasmic proteins was initially identified as signaling adaptors that bind directly to the intracellular domains of receptors of the TNF-R superfamily. It is now appreciated that TRAF molecules are widely employed in signaling by a variety of adaptive and innate immune receptors as well as cytokine receptors. TRAF-dependent signaling pathways typically lead to the activation of nuclear factor-κBs (NF-κBs), mitogen-activated protein kinases (MAPKs), or interferon-regulatory factors (IRFs). Most of these signaling pathways have been linked to inflammation, and therefore TRAF molecules were expected to regulate inflammation and inflammatory responses since their discovery in 1990s. However, direct in vivo evidence of TRAFs in inflammation and especially in inflammatory diseases had been lacking for many years, partly due to the difficulty imposed by early lethality of TRAF2-/-, TRAF3-/-, and TRAF6-/- mice. With the creation of conditional knockout and lineage-specific transgenic mice of different TRAF molecules, our understanding about TRAFs in inflammation and inflammatory responses has rapidly advanced during the past decade. Increasing evidence indicates that TRAF molecules are versatile and indispensable regulators of inflammation and inflammatory responses and that aberrant expression or function of TRAFs contributes to the pathogenesis of inflammatory diseases.", "The ectodomain of matrix protein 2 (M2e) is a promising candidate for a broadly protective influenza A vaccine because it is highly conserved and antibodies to M2e are protective in animal models. STF2.4xM2e (VAX102) is a recombinant fusion protein that links four tandem copies of the M2e antigen to Salmonella typhimurium flagellin, a TLR5 ligand used as an adjuvant. The objectives of this first-in-human study were to assess the safety and immunogenicity of VAX102 given as a prime-boost regimen to healthy adults. Sixty subjects 18-49 years old were enrolled in a multicenter, double-blind, randomized, placebo-controlled trial (Study 1). Based on pre-clincial data, initial design included doses starting at 10 μg, with an escalation plan. After reactogenicity was noted at the 10 μg dose, the trial was redesigned to evaluate 0.3, 1.0, and 3 μg doses. Following this study, 16 subjects were enrolled in Study 2, an open label, low dose study, to evaluate doses of 0.03 and 0.1 μg. In both trials, vaccine or placebo was given intramuscularly (i.m.) at 0 and 28 days. Clinical and laboratory safety assessments took place 1 and 7 days after immunization. Immune responses to M2e and flagellin were assessed by ELISA at 7, 14 and 28 days after each dose. Seroconversion was defined as a serum IgG anti-M2e antibody value ≥0.174 μg/ml and a fourfold rise in concentration. Doses of 0.03-1 μg were safe and well tolerated in all subjects. Doses of 0.03 and 0.1 μg produced limited immunogenicity (38% and 75% respectively), after the second dose of vaccine. Doses of 0.3 and 1.0 μg were immunogenic in 18 (75%) of 24 vaccinees after the first dose and 23 (96%) after the second dose. In the 1.0 μg group, the geometric mean M2e antibody concentration was 0.4 μg/ml after the first dose and 1.7 μg/ml after the booster dose. M2e antibody concentrations and seroconversion rates were not significantly different at higher doses (p>0.05). Immune response to flagellin was robust but did not appear to interfere with M2e antibody responses after the booster dose. Following the first injection of VAX102 at higher doses (3 and 10 μg), self-limited but severe symptoms were noted in some subjects and were associated with elevated levels of C-reactive protein. Although not directly measured, this reaction was believed to be mediated by cytokine release. VAX102 was safe and induced high antibody levels to M2e at 0.3 and 1.0 μg doses. The TLR5 ligand, S. typhimurium flagellin, is a novel approach to adjuvant-like activity through activation of innate immunity, and when fused to multiple copies of the M2e protein, the vaccine was able to induce a fourfold rise in antibody in humans, to a previously non-immunogenic, highly-conserved portion of the influenza virus. Clinical correlates of protection that may be afforded by M2e antibody in humans are a future focus of investigation.", "A pooled analysis of the safety of the human papillomavirus (HPV)-16/18 AS04-adjuvanted cervical cancer vaccine Cervarix (GlaxoSmithKline) was performed in a cohort of almost 30,000 girls and women aged > or =10 years, 16,142 who received at least one dose of the HPV-16/18 vaccine and 13,811 who received one of three controls [Al(OH)(3) or hepatitis A vaccine (720 or 360 EU)]. Data are available for a total of 45,988 vaccine doses. Solicited local and general symptoms were recorded for seven days after each dose. Serious adverse events (SAEs), pregnancies, medically significant conditions (MSCs) and new onset of chronic diseases (NOCDs), including new onset of autoimmune diseases (NOADs), were proactively monitored. Data were analyzed by vaccine group according to age (10-14, 15-25 and >25 years) and reporting period (months 0-7, months 7-12 and >month 12). Rates of solicited local and general symptoms were higher in the HPV-16/18 vaccine group than in the control groups. However, compliance with the three-dose schedule was high and did not differ between groups (93.4% for HPV-16/18 vaccine group versus 92.5% for pooled controls). No clinically relevant differences were seen between the HPV-16/18 vaccine and pooled control groups in rates of SAEs (2.8% versus 3.1%), MSCs (19.4% versus 21.4%), NOCDs (1.7% in both groups) or NOADs (0.4% versus 0.3%). Similarly, no differences in pregnancy outcomes or rates of withdrawals due to AEs or SAEs were observed between groups. In conclusion, analysis of this large database shows the HPV-16/18 AS04-adjuvanted cervical cancer vaccine to have a favorable safety profile in women of all ages.", "Alum adjuvants have been in continuous clinical use for more than 80 yr. While the prevailing theory has been that depot formation and the associated slow release of antigen and/or inflammation are responsible for alum enhancement of antigen presentation and subsequent T- and B-cell responses, this has never been formally proven. To examine antigen persistence, we used the chimeric fluorescent protein EαGFP, which allows assessment of antigen presentation in situ, using the Y-Ae antibody. We demonstrate that alum and/or CpG adjuvants induced similar uptake of antigen, and in all cases, GFP signal did not persist beyond 24 h in draining lymph node antigen-presenting cells. Antigen presentation was first detectable on B cells within 6-12 h of antigen administration, followed by conventional dendritic cells (DCs) at 12-24 h, then finally plasmacytoid DCs at 48 h or later. Again, alum and/or CpG adjuvants did not have an effect on the magnitude or sequence of this response; furthermore, they induced similar antigen-specific T-cell activation in vivo. Notably, removal of the injection site and associated alum depot, as early as 2 h after administration, had no appreciable effect on antigen-specific T- and B-cell responses. This study clearly rules out a role for depot formation in alum adjuvant activity." ]
Role of Wnt/-catenin signaling pathway in the restoration of induced pluripotent stem cell-derived retinal pigment epithelium after laser photocoagulation	To investigate the role of Wnt/β-catenin signaling pathway in the restoration of induced pluripotent stem cell-derived retinal pigment epithelium (hiPSC-RPE) after laser photocoagulation. After differentiation of RPE cells from hiPSCs, laser photocoagulation was performed. Activation of Wnt/β-catenin signaling at days 1 and 5 after laser photocoagulation was evaluated by expression of β-catenin. Cell proliferation and alteration in cell-to-cell contact at day 5 after laser photocoagulation with or without Dickkopf-1 (Dkk-1) treatment were studied using ethynyl-2'-deoxyuridine (EdU) assay and zonula occludens-1 (ZO-1) expression analysis, respectively. The mRNA levels of Wnt genes at day 5 after laser photocoagulation were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR). Activation of Wnt/β-catenin signaling at days 1 and 5 after laser photocoagulation was confirmed by β-catenin accumulation in the cytoplasm and nucleus of hiPSC-RPE. Many EdU-positive cells also expressed β-catenin, and the number of EdU-positive cells was decreased at day 5 after laser photocoagulation after Dkk-1 treatment, indicating that Wnt/β-catenin signaling mediated hiPSC-RPE proliferation. ZO-1 expression was not decreased with Dkk-1 treatment at day 5 after laser photocoagulation, indicating that Wnt/β-catenin signaling mediated hiPSC-RPE restoration. At day 5, after laser photocoagulation, mRNA levels of Wnt2b, Wnt3, Wnt5a, Wnt7a, and Wnt10b were increased. Wnt/β-catenin signaling has a crucial role in restoration of hiPSC-RPE proliferation after laser photocoagulation. Manipulation of Wnt/β-catenin signaling while elucidating the underlying mechanisms of RPE restoration might have a therapeutic potential in retinal degenerative diseases.	[ "Mutations in the genes encoding the Wnt receptor Frizzled-4 (FZD4), coreceptor LRP5, or the ligand Norrin disrupt retinal vascular development and cause ophthalmic diseases. Although Norrin is structurally unrelated to Wnts, it binds FZD4 and activates the canonical Wnt pathway. Here we show that the tetraspanin Tspan12 is expressed in the retinal vasculature, and loss of Tspan12 phenocopies defects seen in Fzd4, Lrp5, and Norrin mutant mice. In addition, Tspan12 genetically interacts with Norrin or Lrp5. Overexpressed TSPAN12 associates with the Norrin-receptor complex and significantly increases Norrin/beta-catenin but not Wnt/beta-catenin signaling, whereas Tspan12 siRNA abolishes transcriptional responses to Norrin but not Wnt3A in retinal endothelial cells. Signaling defects caused by Norrin or FZD4 mutations that are predicted to impair receptor multimerization are rescued by overexpression of TSPAN12. Our data indicate that Norrin multimers and TSPAN12 cooperatively promote multimerization of FZD4 and its associated proteins to elicit physiological levels of signaling.", "The aim of this study is to assess the role of Frizzled-4 (FZD4) in familial exudative vitreoretinopathy (FEVR) and Coats disease. Tissue samples were collected for DNA extraction and automated DNA sequencing of the two coding exons of FZD4 in both directions. Cases carrying a FZD4 mutation and demonstrating extreme disease severity were selected for direct automated sequencing of all coding exons of LRP5, NDP and TSPAN12. Clinical data were obtained for the purpose of identifying genotype-phenotype correlations. 68 probands were diagnosed as having autosomal dominant or sporadic FEVR. Eleven FZD4 mutations (five missense, three deletions, one insertion, two nonsense) were identified. Six of these mutations are novel, and none were found in 346 control chromosomes. In 16 cases of Coats disease, one polymorphism combination was found in two samples: no mutations were detected. No genotype-phenotype correlation emerged. Three severely affected cases with FZD4 mutations failed to show additional mutations in the three other FEVR genes. The authors identified 12 FEVR probands with FZD4 mutations. FZD4 mutation screening can be a useful tool especially in mild or atypical cases of FEVR. Germ-line mutations in FZD4 do not appear to be a common cause of Coats disease.", "Disorders of retinal vascular growth and function are responsible for vision loss in a variety of diseases, including diabetic retinopathy, age-related macular degeneration, retinopathy of prematurity and retinal artery or vein occlusion. Over the past decade, a new signaling pathway that controls retinal vascular development has emerged from the study of inherited disorders - in both humans and mice - that are characterized by retinal hypovascularization. This pathway utilizes a glial-derived extracellular ligand, Norrin, that acts on a transmembrane receptor, Frizzled4, a coreceptor, Lrp5, and an auxiliary membrane protein, Tspan12, on the surface of developing endothelial cells. The resulting signal controls a transcriptional program that regulates endothelial growth and maturation. It will be of great interest to determine whether modulating this pathway could represent a therapeutic approach to human retinal vascular disease.", "Wnt-signaling, a ubiquitous pathway that directs differentiation, cell polarity, and tissue specificity, has been implicated as an important gene-expression pathway in retinal development. An increasing body of evidence supports the importance of Wnt-signaling, and specifically, norrin-mediated Wnt-signaling in retinal development and retinal maintenance. Gene mutations affecting the Wnt-signaling pathways result in a variety of inherited vitreoretinopathies. Additionally, there is growing evidence that prematurity and associated retinopathy are associated with alterations in the Wnt-signaling pathways. Further investigations may allow for improved diagnoses, management, and therapies in the future.", "Inherited retinal diseases, such as age-related macular degeneration and retinitis pigmentosa, are the leading cause of blindness in the developed world. Currently, treatments for these conditions are limited. Recently, considerable attention has been given to the possibility of using patient-specific induced pluripotent stem cells (iPSCs) as a treatment for these conditions. iPSCs reprogrammed from adult somatic cells offer the possibility of generating patient-specific cell lines in vitro. In this review, we will discuss the current literature pertaining to iPSC modeling of retinal disease, gene therapy of iPSC-derived retinal pigmented epithelium (RPE) cells, and retinal transplantation. We will focus on the use of iPSCs created from patients with inherited eye diseases for testing the efficacy of gene or drug-based therapies, elucidating previously unknown mechanisms and pathways of disease, and as a source of autologous cells for cell replacement.", "Norrin/Frizzled4 (Fz4) signaling activates the canonical Wnt pathway to control retinal vascular development. Using genetically engineered mice, we show that precocious Norrin production leads to premature retinal vascular invasion and delayed Norrin production leads to characteristic defects in intraretinal vascular architecture. In genetic mosaics, wild-type endothelial cells (ECs) instruct neighboring Fz4(-/-) ECs to produce an architecturally normal mosaic vasculature, a cell nonautonomous effect. However, over the ensuing weeks, Fz4(-/-) ECs are selectively eliminated from the mosaic vasculature, implying the existence of a quality control program that targets defective ECs. In the adult retina and cerebellum, gain or loss of Norrin/Fz4 signaling results in a cell-autonomous gain or loss, respectively, of blood retina barrier and blood brain barrier function, indicating an ongoing requirement for Frizzled signaling in barrier maintenance and substantial plasticity in mature CNS vascular structure.", "Familial exudative vitreoretinopathy (FEVR) is a rare inherited disorder of retinal angiogenesis. Cases can be autosomal dominant, autosomal recessive, or X-linked. FEVR patients have an avascular peripheral retina which, depending on the degree of ischaemia, causes the secondary complications of the disease. Expressivity may be asymmetric and is highly variable. Five genes have been identified that when mutated, cause FEVR; NDP (X-linked), FZD4 (autosomal dominant and recessive), LRP5 (autosomal dominant and recessive), TSPAN12 (autosomal dominant and recessive), and ZNF408 (autosomal dominant). Four of these genes have been shown to have a central role in Norrin/Frizzled4 signalling, suggesting a critical role for this pathway in retinal angiogenesis. In addition to the ocular features, LRP5 mutations can cause osteopenia and osteoporosis. All FEVR patients in whom molecular testing is not easily accessible should have dual energy X-ray absorptiometry (DEXA) scans to assess bone mineral density, as treatment can be initiated to reduce the risk of bone fractures." ]
Down-regulation of long non-coding RNA snaR in human papillomaviruses-negative cervical squamous cell carcinoma	Long non-coding RNAs (lncRNAs) snaR is a newly identified lncRNA with known functionality only in colon cancer. Our study was carried out to investigate the involvement of lncRNA snaR in human papillomaviruses (HPV)-negative cervical squamous cell carcinoma (CSCC). In the present study, plasma levels of lncRNA snaR in 108 patients with HPV-negative CSCC at stage I and II, and 35 healthy female controls were detected by real-time quantitative PCR. ROC curve analysis was performed to evaluate the diagnostic value of lncRNA snaR for HPV-negative CSCC. All patients were subjected to surgical resection and followed-up for 5 years to record cancer recurrence. lncRNA snaR expression vectors were transfected into HPV-negative CSCC cells. Cell migration and invasion ability were evaluated by Transwell migration and invasion assay, respectively. Expression levels of TGF-β1 were determined by Western blot. It was observed that lncRNA snaR was down-regulated in HPV-negative CSCC patients comparing with healthy controls. Down-regulation of lncRNA snaR effectively distinguished HPV-negative CSCC patients from healthy controls. lncRNA snaR was further down-regulated in patients with distant recurrence (DR) but not in patients with local-recurrence or without recurrence. lncRNA snaR overexpression decreased TGF-β1 expression in CSCC cells, while exogenous TGF-β1 treatment showed no significant effects on lncRNA snaR expression. lncRNA snaR overexpression inhibited cancer cell migration and invasion, while TGF-β1 treatment attenuated the inhibitory effect of lncRNA snaR overexpression on cancer cell migration and invasion. We therefore conclude that down-regulation of lncRNA snaR may induce postoperative DR of HPV-negative CSCC possibly through the interactions with TGF-β1.	[ "Human papillomavirus vaccines prevent human papillomavirus infection and cervical precancers. The impact of vaccinating women with a current infection or after treatment for an human papillomavirus-associated lesion is not fully understood. To determine whether human papillomavirus-16/18 vaccination influences the outcome of infections present at vaccination and the rate of infection and disease after treatment of lesions. We included 1711 women (18-25 years) with carcinogenic human papillomavirus infection and 311 women of similar age who underwent treatment for cervical precancer and who participated in a community-based trial of the AS04-adjuvanted human papillomavirus-16/18 virus-like particle vaccine. Participants were randomized (human papillomavirus or hepatitis A vaccine) and offered 3 vaccinations over 6 months. Follow-up included annual visits (more frequently if clinically indicated), referral to colposcopy of high-grade and persistent low-grade lesions, treatment by loop electrosurgical excisional procedure when clinically indicated, and cytologic and virologic follow-up after treatment. Among women with human papillomavirus infection at the time of vaccination, we considered type-specific viral clearance, and development of cytologic (squamous intraepithelial lesions) and histologic (cervical intraepithelial neoplasia) lesions. Among treated women, we considered single-time and persistent human papillomavirus infection, squamous intraepithelial lesions, and cervical intraepithelial neoplasia 2 or greater. Outcomes associated with infections absent before treatment also were evaluated. Infection-level analyses were performed and vaccine efficacy estimated. Median follow-up was 56.7 months (women with human papillomavirus infection) and 27.3 months (treated women). There was no evidence of vaccine efficacy to increase clearance of human papillomavirus infections or decrease incidence of cytologic/histologic abnormalities associated with human papillomavirus types present at enrollment. Vaccine efficacy for human papillomavirus 16/18 clearance and against human papillomavirus 16/18 progression from infection to cervical intraepithelial neoplasia 2 or greater were -5.4% (95% confidence interval -19,10) and 0.3% (95% confidence interval -69,41), respectively. Among treated women, 34.1% had oncogenic infection and 1.6% had cervical intraepithelial neoplasia 2 or greater detected after treatment, respectively, and of these 69.8% and 20.0% were the result of new infections. We observed no significant effect of vaccination on rates of infection/lesions after treatment. Vaccine efficacy estimates for human papillomavirus 16/18 associated persistent infection and cervical intraepithelial neoplasia 2 or greater after treatment were 34.7% (95% confidence interval -131, 82) and -211% (95% confidence interval -2901, 68), respectively. We observed evidence for a partial and nonsignificant protective effect of vaccination against new infections absent before treatment. For incident human papillomavirus 16/18, human papillomavirus 31/33/45, and oncogenic human papillomavirus infections post-treatment, vaccine efficacy estimates were 57.9% (95% confidence interval -43, 88), 72.9% (95% confidence interval 29, 90), and 36.7% (95% confidence interval 1.5, 59), respectively. We find no evidence for a vaccine effect on the fate of detectable human papillomavirus infections. We show that vaccination does not protect against infections/lesions after treatment. Evaluation of vaccine protection against new infections after treatment and resultant lesions warrants further consideration in future studies.", "PCGEM1 is a novel, highly prostate tissue-specific, androgen-regulated gene. Here, we demonstrate that PCGEM1 expression is significantly higher in prostate cancer (CaP) cells of African-American men than in Caucasian-American men (P=0.0002). Further, increased PCGEM1 expression associates with normal prostate epithelial cells of CaP patients with a family history of CaP (P=0.0400). PCGEM1 overexpression in LNCaP and in NIH3T3 cells promotes cell proliferation and a dramatic increase in colony formation, suggesting a biological role of PCGEM1 in cell growth regulation. Taken together, the cell proliferation/colony formation-promoting functions of PCGEM1 and the association of its increased expression with high-risk CaP patients suggest the potential roles of PCGEM1 in CaP onset/progression, especially in these high-risk groups.", "The human IGF2-P4 and H19 promoters are highly active in a variety of human cancers (including bladder cancer), while existing at a nearly undetectable level in the surrounding normal tissue.Single promoter vectors expressing diphtheria toxin A-fragment (DTA) under the control regulation of IGF2-P4 or H19 regulatory sequences (IGF2-P4-DTA and H19-DTA) were previously successfully used in cell lines, animal models and recently in human patients with superficial cell carcinoma of the bladder (treated with H19-DTA). However this targeted medicine approach could be limited, as not all cancer patients express high levels of H19. Hence, a double promoter DTA-expressing vector was created, carrying on a single construct two separate genes expressing the diphtheria toxin A-fragment (DTA), from two different regulatory sequences, selected from the cancer-specific promoters H19 and IGF2-P4. H19 and IGF2-P4 gene expression was tested in samples of Transitional Cell Carcinoma (TCC) of the bladder by in-situ hybridization (ISH) and by quantitative Real-Time PCR (qRT-PCR). The therapeutic potential of the double promoter toxin vector H19-DTA-IGF2-P4-DTA was tested in TCC cell lines and in heterotopic and orthotopic animal models of bladder cancer. Nearly 100% of TCC patients highly expressed IGF2-P4 and H19, as determined by ISH and by qRT-PCR. The double promoter vector exhibited superior tumor growth inhibition activity compared to the single promoter expression vectors, in cell lines and in heterotopic and orthotopic bladder tumors. Our findings show that bladder tumors may be successfully treated by intravesical instillation of the double promoter vector H19-DTA-P4-DTA.Overall, the double promoter vector exhibited enhanced anti-cancer activity relative to single promoter expression vectors carrying either gene alone.", "Noncoding RNAs (ncRNA) participate in epigenetic regulation but are poorly understood. Here we characterize the transcriptional landscape of the four human HOX loci at five base pair resolution in 11 anatomic sites and identify 231 HOX ncRNAs that extend known transcribed regions by more than 30 kilobases. HOX ncRNAs are spatially expressed along developmental axes and possess unique sequence motifs, and their expression demarcates broad chromosomal domains of differential histone methylation and RNA polymerase accessibility. We identified a 2.2 kilobase ncRNA residing in the HOXC locus, termed HOTAIR, which represses transcription in trans across 40 kilobases of the HOXD locus. HOTAIR interacts with Polycomb Repressive Complex 2 (PRC2) and is required for PRC2 occupancy and histone H3 lysine-27 trimethylation of HOXD locus. Thus, transcription of ncRNA may demarcate chromosomal domains of gene silencing at a distance; these results have broad implications for gene regulation in development and disease states.", "Recent genome-wide association studies reported strong and reproducible associations of multiple genetic variants in a large \"gene-desert\" region of chromosome 8q24 with susceptibility to prostate cancer (PC). However, the causative or functional variants of these 8q24 loci and their biological mechanisms associated with PC susceptibility remain unclear and should be investigated. Here, focusing on its most centromeric region (so-called Region 2: Chr8: 128.14-128.28 Mb) among the multiple PC loci on 8q24, we performed fine mapping and re-sequencing of this critical region and identified SNPs (single nucleotide polymorphisms) between rs1456315 and rs7463708 (chr8: 128,173,119-128,173,237 bp) to be most significantly associated with PC susceptibility (P = 2.00 × 10(-24) , OR = 1.74, 95% confidence interval = 1.56-1.93). Importantly, we show that this region was transcribed as a ∼13 kb intron-less long non-coding RNA (ncRNA), termed PRNCR1 (prostate cancer non-coding RNA 1), and PRNCR1 expression was upregulated in some of the PC cells as well as precursor lesion prostatic intraepithelial neoplasia. Knockdown of PRNCR1 by siRNA attenuated the viability of PC cells and the transactivation activity of androgen receptor, which indicates that PRNCR1 could be involved in prostate carcinogenesis possibly through androgen receptor activity. These findings could provide a new insight in understanding the pathogenesis of genetic factors for PC susceptibility and prostate carcinogenesis.", "With the advent of next generation sequencing methods and progress in transcriptome analysis, it became obvious that the human genome contains much more than just protein-coding genes. In fact, up to 70% of our genome is transcribed into RNA that does not serve as templates for proteins. In this review, we focus on the emerging roles of these long non-coding RNAs (lncRNAs) in the field of tumor biology. Long ncRNAs were found to be deregulated in several human cancers and show tissue-specific expression. Functional studies revealed a broad spectrum of mechanisms applied by lncRNAs such as HOTAIR, MALAT1, ANRIL or lincRNA-p21 to fulfill their functions. Here, we link the cellular processes influenced by long ncRNAs to the hallmarks of cancer and therefore provide an ncRNA point-of-view on tumor biology. This should stimulate new research directions and therapeutic options considering long ncRNAs as novel prognostic markers and therapeutic targets.", "The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence." ]
Non-HDMTX-based treatment of metastatic osteosarcoma in India and low-income countries	Metastatic osteosarcoma is largely treated with high-dose methotrexate (HDMTX)-based therapy, especially in the pediatric population. This mandates complex pharmacokinetic monitoring in a costly inpatient setting to mitigate unpredictable serious toxicities. Hence, a non-HDMTX-based regimen is worth exploring, especially in India and low- and middle-income countries.	[ "Ifosfamide is an active chemotherapeutic agent in a wide range of gynecologic tumors; favorable response rates have been reported in ovarian (epithelial and germ cell), uterine, and cervical neoplasms. Central neurotoxicity is a known, but poorly described side effect. We report 23 patients who received a total of 75 cycles of ifosfamide, either as a single agent or in combination with other chemotherapeutic agents. Six of twenty-three (26%) experienced grade 4 neurotoxicity; clinical presentation included confusion, aphasia, hallucinations, and coma. All patients exhibited the first evidence of neurotoxicity by the end of the 24-hr infusion. Three of six patients with grade 4 neurotoxicity expired within 14 days of receiving ifosfamide. The neurotoxicity resolved over 2 to 4 days in the remaining patients. Serum albumin was normal (greater than 3.5 g/dl) in 63 cycles of ifosfamide not associated with neurotoxicity. When serum albumin was less than 3.5 g/dl, 6 of 12 cycles were associated with severe neurotoxicity (P less than 0.001). Low serum albumin (less than 3.5 g/dl) appears to be associated with a high risk of severe neurotoxicity in patients receiving single-dose ifosfamide therapy.", "High-dose methotrexate (doses ≥1 g/m(2)) is a key component of several chemotherapy regimens used to treat patients with leukemia or lymphoma. Despite appropriate precautions with hydration, urine alkalinization, and leucovorin, nephrotoxicity remains a risk which can lead to significant morbidity and mortality. Current reports of risk factors for nephrotoxicity focus on patients with nephrotoxicity with a lack of comparison to those without toxicity. This study aimed to describe the incidence of high-dose methotrexate-induced nephrotoxicity at our institution and determined risk factors for high-dose methotrexate-induced nephrotoxicity by examining characteristics of patients with and without nephrotoxicity. This was a retrospective, single-center, chart review. Adult patients with a diagnosis of leukemia or lymphoma who received high-dose methotrexate were included. Serum creatinine values were used to evaluate nephrotoxicity according to Common Terminology Criteria for Adverse Events criteria v4.03. Data related to the following proposed risk factors were collected: age, sex, body mass index, methotrexate dose, number of high-dose methotrexate exposures, leucovorin administration route, baseline renal function, albumin, hydration status, Clostridium difficile infection, urine pH, and concomitant interacting and nephrotoxic medications. The primary endpoint was evaluated with exact binomial methods and risk factors were identified using multivariable random-effects logistic regression. Final analyses included 140 patients with 432 high-dose methotrexate exposures. There were no differences in baseline demographical characteristics. Fifty-four patients (38.6%) experienced nephrotoxicity of any grade: 27.9% with grade 1, 5.7% with grade 2, 3.6% grade 3, 0% with grade 4, and 1.4% with grade 5 toxicity. More patients in the toxicity group received doses of methotrexate ≥3 g/m(2) (58.3% versus 57.2%, p < 0.001), had an albumin level <3 g/dL (31.9% versus 15.9%, p = 0.04), and received an interacting medication during high-dose methotrexate clearance (44.4% versus 24.7%, p = 0.003). Male gender (OR 2.3, 95% CI: 1.27-4.18, p = 0.006), albumin (OR 0.44, 95% CI: 0.26-0.75, p = 0.002), number of drug interactions (OR 1.60, 95% CI: 1.15-2.21, p = 0.005), and use of furosemide (OR 2.56, 95% CI 1.46-4.48, p = 0.001) were all independent risk factors for the development of nephrotoxicity. Nephrotoxicity is a possible complication of therapy with high-dose methotrexate with most instances comprising grade 1-2 toxicity. Male gender, low albumin, and administration of interacting drugs or furosemide during high-dose methotrexate clearance may predispose patients to nephrotoxicity.", "As a weak acid, methotrexate (MTX) is bound to serum albumin and has variable protein binding. The purpose of this study was to assess serum albumin's relationship with MTX pharmacokinetics by comparing MTX clearance and toxicities between patients with normal serum albumin to those with hypoalbuminemia. This single-center retrospective study included adult patients with leukemia or lymphoma who received their first MTX at a dose ≥1 g/m2. Hypoalbuminemia was defined as serum albumin ≤3.4 g/dL. MTX clearance was defined as the first documented time the MTX level ≤0.05 μM. Fisher's exact tests and Wilcoxon rank sum tests were used to examine differences in toxicities, and Cox proportional hazard regression was used to assess relationship with time to clearance. Of 523 patients identified, 167 patients were evaluable. One hundred thirty-five patients had normal serum albumin and 32 had hypoalbuminemia. Hypoalbuminemia was associated with a higher proportion of patients experiencing edema, ascites or pleural effusions (34 vs. 12 %, p = 0.006), and the concomitant use of nephrotoxic agents (41 vs. 20 %, p = 0.021). Hypoalbuminemia was associated with a significantly longer time to MTX clearance (median 96 vs. 72 h, p = 0.004). In addition, patients with hypoalbuminemia had a higher proportion of hyperbilirubinemia and significantly longer hospitalization (median 14 vs. 5 days, p < 0.001). In conclusion, hypoalbuminemia was associated with increased time to MTX clearance and increased length of hospitalization. High dose MTX is safe to administer in patients with low albumin levels, with appropriate leucovorin rescue, and good supportive care.", "The experimental data supporting and opposing the use of intravenous albumin in various groups of patients are provided, and conclusions are drawn from these data. The metabolism and kinetics of albumin are reviewed, and the importance of albumin levels in critically ill patients is discussed. The reviewed literature supports the conclusion that in most critically ill patients, intravenous albumin does not improve outcome." ]
Effect of Roux-en-Y gastric bypass on beta cell function in patients with type 2 diabetes	Roux-en-Y gastric bypass results in large and sustained weight loss and resolution of type 2 diabetes in 60% of cases at 1-2 years. In addition to calorie restriction and weight loss, various gastro-intestinal mediated mechanisms, independent of weight loss, also contribute to glucose control. The anatomical re-arrangement of the small intestine after gastric bypass results in accelerated nutrient transit, enhances the release of post-prandial gut hormones incretins and of insulin, alters the metabolism and the entero-hepatic cycle of bile acids, modifies intestinal glucose uptake and metabolism, and alters the composition and function of the microbiome. The amelioration of beta cell function after gastric bypass in individuals with type 2 diabetes requires enteric stimulation. However, beta cell function in response to intravenous glucose stimulus remains severely impaired, even in individuals in full clinical diabetes remission. The permanent impairment of the beta cell may explain diabetes relapse years after surgery.	[ "Surgery is the most effective treatment of morbid obesity and leads to dramatic improvements in type 2 diabetes mellitus (T2DM). Gastrointestinal metabolic surgery has been proposed as a treatment option for T2DM. However, a grading system to categorize and predict the outcome of metabolic surgery is lacking. The study setting was a tertiary referral hospital (Taoyuan City, Taoyuan County, Taiwan). We first evaluated 63 patients and identified 4 factors that predicted the success of T2DM remission after bariatric surgery in this cohort: body mass index, C-peptide level, T2DM duration, and patient age. We used these variables to construct the Diabetes Surgery Score, a multidimensional 10-point scale along which greater scores indicate a better chance of T2DM remission. We then validated the index in a prospective collected cohort of 176 patients, using remission of T2DM at 1 year after surgery as the outcome variable. A total of 48 T2DM remissions occurred among the 63 patients and 115 remissions (65.3%) in the validation cohort. Patients with T2DM remission after surgery had a greater Diabetes Surgery Score than those without (8 ± 4 versus 4 ± 4, P < .05). Patients with a greater Diabetes Surgery Score also had a greater rate of success with T2DM remission (from 33% at score 0 to 100% at score 10); A 1-point increase in the Diabetes Surgery Score translated to an absolute 6.7% in the success rate. The Diabetes Surgery Score is a simple multidimensional grading system that can predict the success of T2DM treatment using bariatric surgery among patients with inadequately controlled T2DM.", "Biliopancreatic diversion (BPD) improves insulin sensitivity and decreases serum cholesterol out of proportion with weight loss. Mechanisms of these effects are unknown. One set of proposed contributors to metabolic improvements after bariatric surgeries is bile acids (BAs). We investigated the early and late effects of BPD on plasma BA levels, composition, and markers of BA synthesis in 15 patients with type 2 diabetes (T2D). We compared these to the early and late effects of Roux-en-Y gastric bypass (RYGB) in 22 patients with T2D and 16 with normal glucose tolerance. Seven weeks after BPD, insulin sensitivity had doubled and serum cholesterol had halved. At this time, BA synthesis markers and total plasma BAs, particularly unconjugated BAs, had markedly risen; this effect could not be entirely explained by low FGF19. In contrast, after RYGB, insulin sensitivity improved gradually with weight loss and cholesterol levels declined marginally; BA synthesis markers were decreased at an early time point (2 weeks) after surgery and returned to the normal range 1 year later. These findings indicate that BA synthesis contributes to the decreased serum cholesterol after BPD. Moreover, they suggest a potential role for altered enterohepatic circulation of BAs in improving insulin sensitivity and cholesterol metabolism after BPD.", "Bariatric surgery provides substantial, sustained weight loss and major improvements in glycaemic control in severely obese individuals with type 2 diabetes. However, uptake of surgery in eligible patients is poor, and the barriers are difficult to surmount. We examine the indications for and efficacy and safety of conventional bariatric surgical procedures and their effect on glycaemic control in type 2 diabetes. How surgical gastrointestinal interventions achieve these changes is of great research interest, and is evolving rapidly. Old classifications about restriction and malabsorption are inadequate, and we explore understanding of putative mechanisms. Some bariatric procedures improve glycaemic control in people with diabetes beyond that expected for weight loss, and understanding this additional effect could provide insights into the pathogenesis of type 2 diabetes and assist in the development of new procedures, devices, and drugs both for obese and non-obese patients.", "Obesity is a risk factor for diabetes, cardiovascular disease events, cancer and overall mortality. Weight loss may protect against these conditions, but robust evidence for this has been lacking. The Swedish Obese Subjects (SOS) study is the first long-term, prospective, controlled trial to provide information on the effects of bariatric surgery on the incidence of these objective endpoints. The SOS study involved 2010 obese subjects who underwent bariatric surgery [gastric bypass (13%), banding (19%) and vertical banded gastroplasty (68%)] and 2037 contemporaneously matched obese control subjects receiving usual care. The age of participants was 37-60 years and body mass index (BMI) was ≥34 kg m(-2) in men and ≥38 kg m(-2) in women. Here, we review the key SOS study results published between 2004 and 2012. Follow-up periods varied from 10 to 20 years in different reports. The mean changes in body weight after 2, 10, 15 and 20 years were -23%, -17%, -16% and -18% in the surgery group and 0%, 1%, -1% and -1% in the control group respectively. Compared with usual care, bariatric surgery was associated with a long-term reduction in overall mortality (primary endpoint) [adjusted hazard ratio (HR) = 0.71, 95% confidence interval (CI) 0.54-0.92; P = 0.01] and decreased incidences of diabetes (adjusted HR=0.17; P < 0.001), myocardial infarction (adjusted HR = 0.71; P = 0.02), stroke (adjusted HR=0.66; P = 0.008) and cancer (women: adjusted HR = 0.58; P = 0.0008; men: n.s.]. The diabetes remission rate was increased severalfold at 2 years [adjusted odds ratio (OR) = 8.42; P < 0.001] and 10 years (adjusted OR = 3.45; P < 0.001). Whereas high insulin and/or high glucose at baseline predicted favourable treatment effects, high baseline BMI did not, indicating that current selection criteria for bariatric surgery need to be revised.", "Glycemic targets in diabetes have been developed to minimize complication risk. Patients with heterozygous, inactivating glucokinase (GCK) mutations have mild fasting hyperglycemia from birth, resulting in an elevated glycated hemoglobin (HbA1c) level that mimics recommended levels for type 1 and type 2 diabetes. To assess the association between chronic, mild hyperglycemia and complication prevalence and severity in patients with GCK mutations. Cross-sectional study in the United Kingdom between August 2008 and December 2010. Assessment of microvascular and macrovascular complications in participants 35 years or older was conducted in 99 GCK mutation carriers (median age, 48.6 years), 91 nondiabetic, familial, nonmutation carriers (control) (median age, 52.2 years), and 83 individuals with young-onset type 2 diabetes (YT2D), diagnosed at age 45 years or younger (median age, 54.7 years). Prevalence and severity of nephropathy, retinopathy, peripheral neuropathy, peripheral vascular disease, and cardiovascular disease. Median HbA1c was 6.9% in patients with the GCK mutation, 5.8% in controls, and 7.8% in patients with YT2D. Patients with GCK had a low prevalence of clinically significant microvascular complications (1% [95% CI, 0%-5%]) that was not significantly different from controls (2% [95% CI, 0.3%-8%], P=.52) and lower than in patients with YT2D (36% [95% CI, 25%-47%], P<.001). Thirty percent of patients with GCK had retinopathy (95% CI, 21%-41%) compared with 14% of controls (95% CI, 7%-23%, P=.007) and 63% of patients with YT2D (95% CI, 51%-73%, P<.001). Neither patients with GCK nor controls required laser therapy for retinopathy compared with 28% (95% CI, 18%-39%) of patients with YT2D (P<.001). Neither patients with GCK patients nor controls had proteinuria and microalbuminuria was rare (GCK, 1% [95% CI, 0.2%-6%]; controls, 2% [95% CI, 0.2%-8%]), whereas 10% (95% CI, 4%-19%) of YT2D patients had proteinuria (P<.001 vs GCK) and 21% (95% CI, 13%-32%) had microalbuminuria (P<.001). Neuropathy was rare in patients with GCK (2% [95% CI, 0.3%-8%]) and controls (95% CI, 0% [0%-4%]) but present in 29% (95% CI, 20%-50%) of YT2D patients (P<.001). Patients with GCK had a low prevalence of clinically significant macrovascular complications (4% [95% CI, 1%-10%]) that was not significantly different from controls (11% [95% CI, 5%-19%]; P=.09), and lower in prevalence than patients with YT2D (30% [95% CI, 21%-41%], P<.001). Despite a median duration of 48.6 years of hyperglycemia, patients with a GCK mutation had low prevalence of microvascular and macrovascular complications. These findings may provide insights into the risks associated with isolated, mild hyperglycemia.", "Metabolic/bariatric procedures for the treatment of morbid obesity, as well as for type 2 diabetes, are among the most commonly performed gastrointestinal operations today, justifying periodic assessment of the numerical status of metabolic/bariatric surgery and its relative distribution of procedures. An email questionnaire was sent to the leadership of the 50 nations or national groupings in the International Federation for the Surgery of Obesity and Metabolic Disorders (IFSO). Outcome measurements were numbers of metabolic/bariatric operations and surgeons, types of procedures performed, and trends from 2003 to 2008 to 2011 worldwide and in the regional groupings of Europe, USA/Canada, Latin/South America, and Asia/Pacific. Response rate was 84%. The global total number of procedures in 2011 was 340,768; the global total number of metabolic/bariatric surgeons was 6,705. The most commonly performed procedures were Roux-en-Y gastric bypass (RYGB) 46.6%; sleeve gastrectomy (SG) 27.8%; adjustable gastric banding (AGB) 17.8%; and biliopancreatic diversion/duodenal switch (BPD/DS) 2.2%. The global trends from 2003 to 2008 to 2011 showed a decrease in RYGB: 65.1 to 49.0 to 46.6%; an increase, followed by a steep decline, in AGB: 24.4 to 42.3 to 17.8%; and a marked increase in SG: 0.0 to 5.3 to 27.89%. BPD/DS declined: 6.1 to 4.9 to 2.1%. The trends from the four IFSO regions differed, except for the universal increase in SG. Periodic metabolic/bariatric surgery surveys add to the knowledge and understanding of all physicians caring for morbidly obese patients. The salient message of the 2011 assessment is that SG (0.0% in 2008) has markedly increased in prevalence.", "Laparoscopic sleeve gastrectomy (LSG) and laparoscopic Roux-en-Y gastric bypass (LRYGB) achieve similar type 2 diabetes mellitus (T2DM) remission rates. Since a great variability exists in defining T2DM remission, an expert panel proposed partial and complete remission criteria that include the maintenance of fasting plasma glucose (FPG) and glycosylated hemoglobin (A1c) objectives for at least 1 year. The 2-year T2DM remission rate and time needed to reach it after LSG or LRYGB were compared using different remission criteria. This was a prospective cohort study of 55 T2DM subjects operated on with LSG (n = 21) or LRYGB (n = 34). Four models for defining remission were used: Buchwald criteria (FPG <100 mg/dl or A1c <6 %), American Diabetes Association (ADA) complete (FPG <100 mg/dl plus A1c <6 % maintained for at least 1 year), ADA partial (FPG <125 mg/dl with A1c <6.5 % maintained for at least 1 year), and ADA complete without time requirement. Both groups were comparable, except for higher A1c levels in the LSG group. The remission rate ranged from 43.6 % using ADA complete remission to 92.7 % with Buchwald criteria, with no differences between surgical procedures. Differences were found in the time to achieve remission only when ADA complete remission criteria (5.1 ± 2.9 months LRYGB and 9.0 ± 3.8 months LSG, p = 0.014) and ADA without time requirement criteria (4.9 ± 2.7 months LRYGB and 8.4 ± 3.9 months LSG, p = 0.005) were used. T2DM remission rate varies widely depending on the criteria used for its definition. Remission occurred sooner after LRYGB when the strictest criteria to define remission were used.", "The goal of the National Institutes of Health-funded American Society for Parenteral and Enteral Nutrition 2017 research workshop (RW) \"Gastric Bypass: Role of the Gut\" was to focus on the exciting research evaluating gut-derived signals in modulating outcomes after bariatric surgery. Although gastric bypass surgery has undoubted positive effects, the mechanistic basis of improved outcomes cannot be solely explained by caloric restriction. Emerging data suggest that bile acid metabolic pathways, luminal contents, energy balance, gut mucosal integrity, as well as the gut microbiota are significantly modulated after bariatric surgery and may be responsible for the variable outcomes, each of which was rigorously evaluated. The RW served as a timely and novel academic meeting that brought together clinicians and researchers across the scientific spectrum, fostering a unique venue for interdisciplinary collaboration among investigators. It promoted engaging discussion and evolution of new research hypotheses and ideas, driving the development of novel ameliorative, therapeutic, and nonsurgical interventions targeting obesity and its comorbidities. Importantly, a critical evaluation of the current knowledge regarding gut-modulated signaling after bariatric surgery, potential pitfalls, and lacunae were thoroughly addressed.", "Obesity and type II diabetes mellitus (T2DM) are closely related and difficult to control by current medical treatment. Bariatric surgery has been proposed for inadequately controlled T2DM in association with obesity. However, prediction of successful T2DM remission after surgery has not been clearly studied in Asian patients. This information might be helpful for applying gastrointestinal surgery as metabolic surgery for T2DM. This was a retrospective clinical study. From January 2002 to December 2008, 88 consecutive patients with morbid obesity, who were enrolled into a surgically supervised weight loss program, and who had T2DM before surgery with at least 1 year complete follow-up data were included. Sixty-eight (77.2%) patients received gastric bypass procedures, and the remaining 20 (22.8%) received restrictive procedures. We analyzed the available information during the initial evaluation of patients who were referred for bariatric surgery, by logistic regression analysis and data mining methods for predictors of successful diabetes remission after surgery. Overall, 68 (77.2%) of the 88 patients had remission of their T2DM 1 year after surgery. Patients in the bypass group had a higher remission rate than those in the restrictive group [59/68 (86.7%) vs. 9/20 (45.0%), p=0.000]. In univariate analysis, patients who had T2DM remission after surgery were younger, heavier, had a wider waist, less severe disease, shorter duration, and higher C-peptide levels than those without remission. Type of operation and T2DM duration remained independent predictors of success after multivariate logistical regression analysis (p<0.000). Data mining analysis confirmed that T2DM duration was the most important predictor. Bariatric surgery is a treatment option for T2DM. Duration of diabetes is the most predictor of success after surgery.", "The close correspondence between energy intake and expenditure over prolonged time periods, coupled with an apparent protection of the level of body adiposity in the face of perturbations of energy balance, has led to the idea that body fatness is regulated via mechanisms that control intake and energy expenditure. Two models have dominated the discussion of how this regulation might take place. The set point model is rooted in physiology, genetics and molecular biology, and suggests that there is an active feedback mechanism linking adipose tissue (stored energy) to intake and expenditure via a set point, presumably encoded in the brain. This model is consistent with many of the biological aspects of energy balance, but struggles to explain the many significant environmental and social influences on obesity, food intake and physical activity. More importantly, the set point model does not effectively explain the 'obesity epidemic'--the large increase in body weight and adiposity of a large proportion of individuals in many countries since the 1980s. An alternative model, called the settling point model, is based on the idea that there is passive feedback between the size of the body stores and aspects of expenditure. This model accommodates many of the social and environmental characteristics of energy balance, but struggles to explain some of the biological and genetic aspects. The shortcomings of these two models reflect their failure to address the gene-by-environment interactions that dominate the regulation of body weight. We discuss two additional models--the general intake model and the dual intervention point model--that address this issue and might offer better ways to understand how body fatness is controlled." ]
Genome-wide transcriptome analysis of tall fescue leaves in saline areas	Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.	[ "Salinity is a major abiotic stress factor limiting crop production. To generate salt-tolerant turf and forage, we had transformed tall fescue (Festuca arundinacea) with AtNHX1, a vacuolar Na(+)/H(+) antiporter gene from Arabidopsis thaliana. In this paper, we report that overexpression of the AtNHX1 gene confers enhanced salt tolerance to the transformed tall fescue progenies. DNA gel blot analysis and reverse transcription (RT) polymerase chain reaction (PCR) were carried out to confirm the inheritance and expression of the AtNHX1 gene in transgenic T(1) and T(2) lines. These transgenic lines showed no phenotypic changes or yield reduction. Plants carrying the AtNHX1 gene were more resistant to a 20 mM NaCl solution than control plants. The roots of the transgenic lines had a higher sodium content than controls, due to an increased Na(+)/H(+) antiporter activity in tonoplast vesicles. Our results suggest that this accumulation of sodium in vacuoles of root cells, mediated by vacuolar Na(+)/H(+) antiporters, reduced the toxic effects of salinity to tall fescue and thus enhanced its salt tolerance.", "Tall fescue (Festuca arundinacea Schreb) is a major cool season forage and turf grass species grown in the temperate regions of the world. In this paper we report the generation of a tall fescue expressed sequence tag (EST) database developed from nine cDNA libraries representing tissues from different plant organs, developmental stages, and abiotic stress factors. The results of inter-library and library-specific in silico expression analyses of these ESTs are also reported. A total of 41,516 ESTs were generated from nine cDNA libraries of tall fescue representing tissues from different plant organs, developmental stages, and abiotic stress conditions. The Festuca Gene Index (FaGI) has been established. To date, this represents the first publicly available tall fescue EST database. In silico gene expression studies using these ESTs were performed to understand stress responses in tall fescue. A large number of ESTs of known stress response gene were identified from stressed tissue libraries. These ESTs represent gene homologues of heat-shock and oxidative stress proteins, and various transcription factor protein families. Highly expressed ESTs representing genes of unknown functions were also identified in the stressed tissue libraries. FaGI provides a useful resource for genomics studies of tall fescue and other closely related forage and turf grass species. Comparative genomic analyses between tall fescue and other grass species, including ryegrasses (Lolium sp.), meadow fescue (F. pratensis) and tetraploid fescue (F. arundinacea var glaucescens) will benefit from this database. These ESTs are an excellent resource for the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) PCR-based molecular markers.", "Plant growth and development are driven by the continuous generation of new cells. Whereas much has been learned at a molecular level about the mechanisms that orchestrate progression through the different cell-cycle phases, little is known about how the cell-cycle machinery operates in the context of an entire plant and contributes to growth, cell differentiation and the formation of new tissues and organs. Here, we discuss how intrinsic developmental signals and environmental cues affect cell-cycle entry and exit.", "Tall fescue (Festuca arundinacea Schreb.) is major cool-season forage and turf grass species worldwide, but high-temperature is a major environmental stress that dramatically threaten forage production and turf management of tall fescue. However, very little is known about the whole-genome molecular mechanisms contributing to thermotolerance. The objectives of this study were to analyzed genome-wide gene expression profiles in the leaves of two tall fescue genotypes, heat tolerant 'PI578718' and heat sensitive 'PI234881' using high-throughput RNA sequencing. A total of 262 million high-quality paired-end reads were generated and assembled into 31,803 unigenes with an average length of 1,840 bp. Of these, 12,974 unigenes showed different expression patterns in response to heat stress and were categorized into 49 Gene Ontology functional subcategories. In addition, the variance of enrichment degree in each functional subcategory between PI578718 and PI234881 increased with increasing treatment time. Cell division and cell cycle genes showed a massive increase in transcript abundance in heat-stressed plants and more activated genes were detected in PI 578718 by Kyoto Encyclopedia of Genes and Genomes pathways analysis. Low molecular weight heat shock protein (LMW-HSP, HSP20) showed activated in two stressed genotypes and high molecular weight HSP (HMW-HSP, HSP90) just in PI578718. Assimilation such as photosynthesis, carbon fixation, CH4, N, S metabolism decreased along with increased dissimilation such as oxidative phosphorylation. The assembled transcriptome of tall fescue could serve as a global description of expressed genes and provide more molecular resources for future functional characterization analysis of genomics in cool-season turfgrass in response to high-temperature. Increased cell division, LMW/HMW-HSP, dissimilation and antioxidant transcript amounts in tall fescue were correlated with successful resistance to high temperature stress.", "We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.", "Plant responses to salt and water stress have much in common. Salinity reduces the ability of plants to take up water, and this quickly causes reductions in growth rate, along with a suite of metabolic changes identical to those caused by water stress. The initial reduction in shoot growth is probably due to hormonal signals generated by the roots. There may be salt-specific effects that later have an impact on growth; if excessive amounts of salt enter the plant, salt will eventually rise to toxic levels in the older transpiring leaves, causing premature senescence, and reduce the photosynthetic leaf area of the plant to a level that cannot sustain growth. These effects take time to develop. Salt-tolerant plants differ from salt-sensitive ones in having a low rate of Na+ and Cl-- transport to leaves, and the ability to compartmentalize these ions in vacuoles to prevent their build-up in cytoplasm or cell walls and thus avoid salt toxicity. In order to understand the processes that give rise to tolerance of salt, as distinct from tolerance of osmotic stress, and to identify genes that control the transport of salt across membranes, it is important to avoid treatments that induce cell plasmolysis, and to design experiments that distinguish between tolerance of salt and tolerance of water stress.", "SCF complexes are the largest family of E3 ubiquitin-protein ligases and mediate the ubiquitination of diverse regulatory and signalling proteins. Here we present the crystal structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF complex, which shows that Cul1 is an elongated protein that consists of a long stalk and a globular domain. The globular domain binds the RING finger protein Rbx1 through an intermolecular beta-sheet, forming a two-subunit catalytic core that recruits the ubiquitin-conjugating enzyme. The long stalk, which consists of three repeats of a novel five-helix motif, binds the Skp1-F boxSkp2 protein substrate-recognition complex at its tip. Cul1 serves as a rigid scaffold that organizes the Skp1-F boxSkp2 and Rbx1 subunits, holding them over 100 A apart. The structure suggests that Cul1 may contribute to catalysis through the positioning of the substrate and the ubiquitin-conjugating enzyme, and this model is supported by Cul1 mutations designed to eliminate the rigidity of the scaffold.", "We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Blast2GO is freely available via Java Web Start at http://www.blast2go.de. http://www.blast2go.de -> Evaluation.", "Longan is a tropical/subtropical fruit tree of great economic importance in Southeast Asia. Progress in understanding molecular mechanisms of longan embryogenesis, which is the primary influence on fruit quality and yield, is slowed by lack of transcriptomic and genomic information. Illumina second generation sequencing, which is suitable for generating enormous numbers of transcript sequences that can be used for functional genomic analysis of longan. In this study, a longan embryogenic callus (EC) cDNA library was sequenced using an Illumina HiSeq 2000 system. A total of 64,876,258 clean reads comprising 5.84 Gb of nucleotides were assembled into 68,925 unigenes of 448-bp mean length, with unigenes ≥1000 bp accounting for 8.26% of the total. Using BLASTx, 40,634 unigenes were found to have significant similarity with accessions in Nr and Swiss- Prot databases. Of these, 38,845 unigenes were assigned to 43 GO sub-categories and 17,118 unigenes were classified into 25 COG sub-groups. In addition, 17,306 unigenes mapped to 199 KEGG pathways, with the categories of Metabolic pathways, Plant-pathogen interaction, Biosynthesis of secondary metabolites, and Genetic information processing being well represented. Analyses of unigenes ≥1000 bp revealed 328 embryogenesis-related unigenes as well as numerous unigenes expressed in EC associated with functions of reproductive growth, such as flowering, gametophytogenesis, and fertility, and vegetative growth, such as root and shoot growth. Furthermore, 23 unigenes related to embryogenesis and reproductive and vegetative growth were validated by quantitative real time PCR (qPCR) in samples from different stages of longan somatic embryogenesis (SE); their differentially expressions in the various embryogenic cultures indicated their possible roles in longan SE. The quantity and variety of expressed EC genes identified in this study is sufficient to serve as a global transcriptome dataset for longan EC and to provide more molecular resources for longan functional genomics.", "To gain insights into molecular mechanisms of grass tolerance to heat stress, we constructed a suppression subtractive cDNA library to identify heat-responsive genes for a C(3) grass species, thermal Agrostis scabra adapted to heat stress in geothermal areas in Yellowstone National Park. Plants were exposed to 20 degrees C (control) or 35 degrees C for 12d. The SSH analysis was performed with control samples as the driver and heat-stressed samples as the tester. Differentially expressed cDNA fragments were cloned to screen the heat up-regulated library. The SSH analysis identified 120 non-redundant putative heat-responsive cDNAs out of 1180 clones. Genes with homology to known proteins were categorized into six functional groups, with the largest group of genes involved in stress/defense, followed by the group of genes related to protein metabolism. Immunoblot analysis confirmed increases in transcripts of selected genes under heat stress. Transcripts of seven and eight genes were strongly enhanced or induced in shoots and roots, respectively, while two genes were only induced in roots under heat stress. The heat up-regulated genes in thermal A. scabra adapted to long-term heat stress are potential candidate genes for engineering stress-tolerant grasses and for revealing molecular mechanisms of grass adaptation to heat stress." ]
In diffusion MRI (dMRI) (dMRI)	In diffusion MRI (dMRI), static magnetic field (B	[ "An automated method for segmenting magnetic resonance head images into brain and non-brain has been developed. It is very robust and accurate and has been tested on thousands of data sets from a wide variety of scanners and taken with a wide variety of MR sequences. The method, Brain Extraction Tool (BET), uses a deformable model that evolves to fit the brain's surface by the application of a set of locally adaptive model forces. The method is very fast and requires no preregistration or other pre-processing before being applied. We describe the new method and give examples of results and the results of extensive quantitative testing against \"gold-standard\" hand segmentations, and two other popular automated methods.", "We propose a method to calculate field maps from the phase of each EPI in an fMRI time series. These field maps can be used to correct the corresponding magnitude images for distortion caused by inhomogeneity in the static magnetic field. In contrast to conventional static distortion correction, in which one 'snapshot' field map is applied to all subsequent fMRI time points, our method also captures dynamic changes to B0 which arise due to motion and respiration. The approach is based on the assumption that the non-B0-related contribution to the phase measured by each radio-frequency coil, which is dominated by the coil sensitivity, is stable over time and can therefore be removed to yield a field map from EPI. Our solution addresses imaging with multi-channel coils at ultra-high field (7T), where phase offsets vary rapidly in space, phase processing is non-trivial and distortions are comparatively large. We propose using dual-echo gradient echo reference scan for the phase offset calculation, which yields estimates with high signal-to-noise ratio. An extrapolation method is proposed which yields reliable estimates for phase offsets even where motion is large and a tailored phase unwrapping procedure for EPI is suggested which gives robust results in regions with disconnected tissue or strong signal decay. Phase offsets are shown to be stable during long measurements (40min) and for large head motions. The dynamic distortion correction proposed here is found to work accurately in the presence of large motion (up to 8.1°), whereas a conventional method based on single field map fails to correct or even introduces distortions (up to 11.2mm). Finally, we show that dynamic unwarping increases the temporal stability of EPI in the presence of motion. Our approach can be applied to any EPI measurements without the need for sequence modification.", "We present, here, a simple method for measurement and correction of off-resonance related geometric distortion in echo-planar imaging (EPI). This method uses high signal-to-noise ratio (SNR) EPI-based field maps, rapidly acquired using a series of gradient recalled images collected across a range of TE values. This field map is distorted in the same manner as the EPI images to be unwarped, providing a direct look-up table for the correct location of each pixel of data. This method adds very little scan time and is robust and easy to implement.", "The advantages of high-resolution diffusion tensor imaging (DTI) have been demonstrated in a recent post-mortem human brain study (Miller et al., NeuroImage 2011;57(1):167-181), showing that white matter fiber tracts can be much more accurately detected in data at a submillimeter isotropic resolution. To our knowledge, in vivo human brain DTI at a submillimeter isotropic resolution has not been routinely achieved yet because of the difficulty in simultaneously achieving high resolution and high signal-to-noise ratio (SNR) in DTI scans. Here we report a 3D multi-slab interleaved EPI acquisition integrated with multiplexed sensitivity encoded (MUSE) reconstruction, to achieve high-quality, high-SNR and submillimeter isotropic resolution (0.85×0.85×0.85mm(3)) in vivo human brain DTI on a 3Tesla clinical MRI scanner. In agreement with the previously reported post-mortem human brain DTI study, our in vivo data show that the structural connectivity networks of human brains can be mapped more accurately and completely with high-resolution DTI as compared with conventional DTI (e.g., 2×2×2mm(3)).", "We present a reconstruction method for phased array multicoil data that is compatible with phase contrast MR angiography. The proposed algorithm can produce either complex difference or phase difference angiograms. Directional flow and quantitative information are preserved with the phase difference reconstruction. The proposed method is computationally efficient and avoids intercoil cancellation errors near the velocity aliasing boundary. Feasibility of the method is demonstrated on human scans." ]
Risk Factors of Superficial Skin Fungal Infections among Primary Schoolchildren in Southern Tanzania	Superficial skin fungal infections are among the neglected communicable diseases in many developing countries. Schoolchildren are among the most affected groups in Southern Tanzania. The main objective of this study was to determine the magnitude and associated risk factors of superficial skin fungal infections among primary schoolchildren in Southern Tanzania.	[ "Oral ketoconazole was given to 50 patients, 36 with superficial and 14 with deep-seated mycoses. Satisfactory results were obtained in dermatophytoses, pityriasis versicolor, and chronic mucocutaneous candidiasis. Paracoccidioidomycosis also responded well to ketoconazole therapy. The authors' experience in patients with histoplasmosis and aspergillosis does not make it possible to express a firm view on the efficacy of the drug. Ketoconazole is not the recommended drug for treatment of sporotrichosis.", "The etiologic agents of the dermatophytoses (ringworm) are classified in three anamorphic (asexual or imperfect) genera, Epidermophyton, Microsporum, and Trichophyton. Species capable of reproducing sexually belong in the teleomorphic genus, Arthroderma, of the Ascomycota. On the basis of primary habitat association, they may be grouped as geophilic (soil associated), zoophilic, and anthropophilic. Adaptation to growth on humans by most geophilic species resulted in diminished loss of sporulation, sexuality, and other soil-associated characteristics. The dermatophytes have the ability to invade keratinized tissue (skin, hair, and nails) but are usually restricted to the nonliving cornified layer of the epidermis because of their inability to penetrate viable tissue of an immunocompetent host. However, invasion does elicit a host response ranging from mild to severe. Acid proteinases, elastase, keratinases, and other proteinases reportedly act as virulence factors. The development of cell-mediated immunity correlated with delayed hypersensitivity and an inflammatory response is associated with clinical cure, whereas the lack of or a defective cell-mediated immunity predisposes the host to chronic or recurrent dermatophyte infection. Chronic dermatophytosis is mostly caused by Trichophyton rubrum, and there is some evidence that mannan produced by this fungus suppresses or diminishes the inflammatory response. Since dermatophytes cause a communicable disease, modes of transmission and control are discussed as well as a survey of recent trends in therapy. Collection of specimens, culture media, and tests for identification are also presented. Genetic studies have led to an understanding of incompatibility mechanisms, pleomorphism and variation, resistance to griseofulvin, and virulence. Molecular biology has contributed to our knowledge of the taxonomy and phylogenetic relationships of dermatophytes.", "The dermatophyte Microsporum gypseum has been shown to produce two siderophores under conditions of low-iron stress. These compounds have been separated as Fe(III) complexes on silica gel, and the principal siderophore has been identified as ferricrocin using the methods of amino acid analysis, comparative thin-layer chromatography, partial sequencing by gas chromatography-mass spectrometry, ultraviolet spectroscopy, and proton nuclear magnetic resonance spectroscopy of the Al(III) complex.", "Dermatophytosis is currently a disease of global importance and a public health burden. It is caused by dermatophytes, which attack and grow on dead animal keratin. Dermatophytes belong to three genera, namely, Epidermophyton, Microsporum, and Trichophyton. The predominant clinical forms and causative agents vary from one region of the world to another. Poor socioeconomic status, high population densities, and poor sanitary conditions are some of the factors responsible for the high prevalence of dermatophytosis in many developing countries, which include countries in southern and eastern Africa, the focus of this review. To the best of our knowledge, there is currently no review article on published findings on dermatophytosis in the eastern and southern parts of Africa. This information will be of interest to the medical and research community since the world has become a global village. This review covers published research findings in eastern and southern regions of Africa until this date. The countries covered in the current review include Kenya, Ethiopia, Tanzania, South Africa, Mozambique, Madagascar, Malawi, Rwanda, Burundi, Uganda, Zambia, Zimbabwe, and Botswana. T. violaceum is the most common human etiological agent in all the countries under review with prevalence ranging from 56.7% to 95%, except for Madagascar (M. langeronii, reclassified as M. audouinii), Uganda (M. gypseum) and Malawi (M. audouinii). Tinea capitis was the most clinical type, followed by tinea corporis. Etiological agents of animal dermatophytoses were variable in the countries where they were reported. Major risk factors for dermatophytoses are age, climatic, and socioeconomic factors.", "Microsporum persicolor, a zoophilic dermatophyte species, is seldom recorded causing human infections in North America. Its identification has been enhanced as a direct result of the development of improved techniques for its characterization. Identifying characteristics include induction of rough-walled macroconidia on sodium chloride-amended medium, absence of good growth at 37 degrees C, and absence of a pH change during growth on casein glucose medium. In contrast, Trichophyton mentagrophytes, a species commonly confused with M. persicolor, has smooth-walled macroconidia, grows well at 37 degrees C, and produces an alkaline reaction on casein glucose medium.", "Dermatophytic fungus infections are common and in the main confined to the stratum corneum. The way the body keeps these infections confined to the stratum corneum involves both nonspecific and specific factors. Cell-mediated immune reactions appear to be the major host defense against invasion. Appropriate cell-mediated immunity not only can limit the spread of dermatophytic fungi but also can rid the fungus from host skin. In contrast, the absence of cell-mediated immunity predisposes to severe and widespread infection and to chronic infection. Complement and polymorphonuclear leukocytes can interact with hyphae once they invade into viable tissue. These interactions are inhibitory to growth. In addition, the inflammation provoked by these interactions can increase epidermal turnover time and thereby force retreat of the fungus back into the stratum corneum or rid the fungus through desquamation. The role of specific antibodies to dermatophytic fungi is uncertain, but it is likely a minor one. High levels of antibodies do not protect against infection or allow resolution of established infection in the absence of other mechanisms. Antibodies may augment complement activation and accumulation of polymorphonuclear leukocytes, but it is unlikely they contribute directly to killing. Indeed, IgE antibodies to dermatophytic fungi develop in many patients with chronic infections.", "Tinea capitis, a disease of children, occurs throughout the United States. We studied 144 clinically diagnosed cases of tinea capitis within a 12-month period. Ninety-six of them had positive cultures; Trichophyton tonsurans grew in 89% and Microsporum organisms in 11%. Ninety-five (99%) of the patients with positive cultures were black, and one (1%) was hispanic. The peak incidence was in the 4-to-5-year age group. Boys and girls were equally affected. Sixty percent of the 96 culture-proved cases were noninflammatory, and 40% were inflammatory (kerions). In four patients, the initial clinical manifestations were severe diffuse seborrhealike scales and crusting of the scalp with minimal alopecia. Mycologic and clinical cure were obtained by a mean of 4.7 weeks of griseofulvin therapy. Neither systemic erythromycin, topical antifungal agents, nor systemic prednisone resulted in earlier eradication. However, prednisone caused the inflammation of the kerions to subside dramatically." ]
Sex is associated with an increased risk of childhood cancer	Male sex is associated with an increased risk of childhood cancer as is high birthweight. Given that sex determination precedes birthweight we conducted a mediation analysis to estimate the direct effect of sex in association with childhood cancer tumor type with birthweight as the mediator.	[ "Male and female differ genetically by their respective sex chromosome composition, that is, XY as male and XX as female. Although both X and Y chromosomes evolved from the same ancestor pair of autosomes, the Y chromosome harbors male-specific genes, which play pivotal roles in male sex determination, germ cell differentiation, and masculinization of various tissues. Deletions or translocation of the sex-determining gene, SRY, from the Y chromosome causes disorders of sex development (previously termed as an intersex condition) with dysgenic gonads. Failure of gonadal development results not only in infertility, but also in increased risks of germ cell tumor (GCT), such as gonadoblastoma and various types of testicular GCT. Recent studies demonstrate that either loss of Y chromosome or ectopic expression of Y chromosome genes is closely associated with various male-biased diseases, including selected somatic cancers. These observations suggest that the Y-linked genes are involved in male health and diseases in more frequently than expected. Although only a small number of protein-coding genes are present in the male-specific region of Y chromosome, the impacts of Y chromosome genes on human diseases are still largely unknown, due to lack of in vivo models and differences between the Y chromosomes of human and rodents. In this review, we highlight the involvement of selected Y chromosome genes in cancer development in men.", "Klinefelter (47,XXY) syndrome occurs in approximately 1:800 male births and accounts for about 10-20% of males attending infertility clinics. Recent studies have shown no obvious phenotypic differences between subjects in which the extra X-chromosome is of paternal or maternal origin; however, a minority of Klinefelter patients are adversely affected clinically and intellectually to an exceptional level, and the underlying basis of this phenotypic variation is not known. We hypothesize that skewed X-inactivation and possibly parental origin of the X-chromosomes is involved. In this study, we determined parental origin and inactivation status of the X-chromosomes in 17 cytogenetically confirmed 47,XXY cases, two 48,XXYY cases and one mosaic 46,XY/47,XXY case. Eight highly polymorphic markers specific to the X-chromosome and the polymorphic human androgen-receptor (HUMARA) methylation assay were used to determine the parental origin and X-inactivation status of the X-chromosomes, respectively. Overall, 17 cases were fully informative, enabling parental origin to be assigned. In 59% of cases, both X-chromosomes were of maternal origin (Xm); in the remaining 41%, one X was of maternal (Xm) and one was of paternal origin (Xp). In 5 of 16 (31%) cases informative at the HUMARA locus, skewed X-inactivation was observed as defined by greater than 80% preferential inactivation involving one of the two X-chromosomes. The two 48,XmXpYY cases both showed preferential paternal X-chromosome (Xp) inactivation. Three 47,XmXmY cases also showed preferential inactivation in one of the two maternal X-chromosomes. These results suggest that skewed X-inactivation in Klinefelter (47,XXY and 48,XXYY) patients may be common and could explain the wide range of mental deficiency and phenotypic abnormalities observed in this disorder. Further studies are warranted to examine the role of X-inactivation and genetic imprinting in Klinefelter patients.", "Rates of cancer in children usually are presented in 5-year age groups, despite large variations of incidence within these groups. The purpose of this report is to provide histology-specific incidence rates within single-year age groups, stratified by sex and race, among children. Data from the National Cancer Institute's SEER Program were used to calculate incidence rates among children younger than 15 years of age at diagnosis. The SEER population denominator file was modified to allow calculation of rates within single years of age. Large differences in rates within 5-year age groups were found for many histologic types. Retinoblastoma and Wilms' tumor, for instance, had up to eight-fold differences. Substantial differences also were observed for non-Hodgkin's lymphoma, neuroblastoma, Hodgkin's disease, acute lymphoid leukemia, acute myeloid leukemia, and osteosarcoma. In general, rates were higher among males than females, although female rates were often higher among young children. Rates of white children were generally higher than those of black children, especially during the first 5 years of life. Embryonal tumors comprised the majority of neoplasms during the first 2 years of life.", "The etiology of childhood cancers remains largely unknown, especially regarding environmental and behavioral risk factors. Unpacking the association between socioeconomic status (SES) and incidence may offer insight into such etiology. We tested associations between SES and childhood cancer incidence in a population-based case-cohort study (source cohort: Minnesota birth registry, 1989-2014). Cases, ages 0-14 years, were linked from the Minnesota Cancer Surveillance System to birth records through probabilistic record linkage. Controls were 4:1 frequency matched on birth year (2,947 cases and 11,907 controls). We tested associations of individual-level (maternal education) and neighborhood-level (census tract composite index) SES using logistic mixed models. In crude models, maternal education was positively associated with incidence of acute lymphoblastic leukemia (odds ratio (OR) = 1.10, 95% confidence interval (CI): 1.02, 1.19), central nervous system tumors (OR = 1.12, 95% CI: 1.04, 1.21), and neuroblastoma (OR = 1.15, 95% CI: 1.02, 1.30). Adjustment for established risk factors-including race/ethnicity, maternal age, and birth weight-substantially attenuated these positive associations. Similar patterns were observed for neighborhood-level SES. Conversely, higher maternal education was inversely associated with hepatoblastoma incidence (adjusted OR = 0.70, 95% CI: 0.51, 0.98). Overall, beyond the social patterning of established demographic and pregnancy-related exposures, SES is not strongly associated with childhood cancer incidence.", "At every age, males have a higher risk of mortality than do females. This sex difference is most often attributed to the usual suspects: differences in hormones and life experiences. However, the fact that XY males have only one X chromosome undoubtedly contributes to this vulnerability, as any mutation that affects a gene on their X chromosome will affect their only copy of that gene. On the other hand, cellular mosaicism created by X inactivation provides a biologic advantage to females. There are 1100 genes on the X chromosome, and most of them are not expressed from the Y chromosome. Therefore, sex differences in the expression of these genes are likely to underlie many sex differences in the expression of diseases affected by these genes. In fact, this genetic biology should be considered for any disease or phenotype that occurs in one sex more than the other, because the disease mechanism may be influenced directly by an X-linked gene or indirectly through the consequences of X inactivation.", "In response to various immune challenges, females show better survival than males; the X chromosome has an important role in this immunological advantage. X chromosome-linked diseases are usually restricted to males, who have only one copy of the X chromosome; however, females are more prone to autoimmune diseases, and the X chromosome may be involved in the breakdown of self tolerance. Several hypotheses have been proposed in recent years that support a role for the X chromosome in shaping autoimmune responses. Here, we review the main mechanisms responsible for increased immune activity in females. This provides a survival advantage in the face of pathogenic insult but can also enhance the susceptibility of females to autoimmunity.", "Binge and heavy drinking are noted in the literature for their relatively high prevalence and adverse health-related effects. We used data from the 2006 Behavioral Risk Factor Surveillance Survey (BRFSS) to determine the associations between binge and heavy drinking and a wide range of health-related variables, including positive and negative health behaviors, preventive care practices, and quality of life indices in a nationally representative sample of 344,793 adults. Rates of binge and heavy drinking in the current sample were 15% and 5%, respectively. Binge and heavy drinking were more common among men, younger adults, and individuals with higher incomes and at least some college education. After controlling for relevant demographic variables, binge and heavy drinking were associated with a number of adverse health-related and preventive care behaviors (e.g., smoking, failing to receive a mammogram), as well as less life satisfaction and a greater number of poor mental health days than those who did not engage in these drinking behaviors. Interestingly, binge and heavy drinking were also associated with some positive health-related variables (e.g., recent physical activity, positive perceptions of one's own health). The current study findings provide additional information regarding the relations between health-related attitudes and behaviors and binge and heavy drinking in the U.S. population. Implications of study findings are discussed." ]
Pseudo-3' Untranslated Regions of Human Pseudogenes Are Under Selective Constraint	The competitive endogenous RNA (ceRNA) hypothesis is an attractively simple model to explain the biological role of many putatively functionless noncoding RNAs. Under this model, there exist transcripts in the cell whose role is to titrate out microRNAs such that the expression level of another target sequence is altered. That it is logistically possible for expression of one microRNA recognition element (MRE)-containing transcript to affect another is seen in the multiple examples of pathogenic effects of inappropriate expression of MRE-containing RNAs. However, the role, if any, of ceRNAs in normal biological processes and at physiological levels is disputed. By comparison of parent genes and pseudogenes we show, both for a specific example and genome-wide, that the pseudo-3' untranslated regions (3'UTRs) of expressed pseudogenes are frequently retained and are under selective constraint in mammalian genomes. We found that the pseudo-3'UTR of BRAFP1, a previously described oncogenic ceRNA, has reduced substitutions relative to its pseudo-coding sequence, and we show sequence constraint on MREs shared between the parent gene, BRAF, and the pseudogene. Investigation of RNA-seq data reveals expression of BRAFP1 in normal somatic tissues in human and in other primates, consistent with biological ceRNA functionality of this pseudogene in nonpathogenic cellular contexts. Furthermore, we find that on a genome-wide scale pseudo-3'UTRs of mammalian pseudogenes (n = 1,629) are under stronger selective constraint than their pseudo-coding sequence counterparts, and are more often retained and expressed. Our results suggest that many human pseudogenes, often considered nonfunctional, may have an evolutionarily constrained role, consistent with the ceRNA hypothesis.	[ "Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other's expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are coupled through miRNAs. This may result in striking effects on a broad range of cellular processes, such as cell differentiation and proliferation. Although several studies have reported the functional relevance of this mechanism of interaction, detailed experiments are lacking that study this phenomenon in controlled conditions by mimicking a physiological range. We used an experimental design based on two bidirectional plasmids and flow cytometry measurements of cotransfected mammalian cells. We validated a stochastic gene interaction model that describes how mRNAs can influence each other's fluctuations in a miRNA-dependent manner in single cells. We show that miRNA-target correlations eventually lead to either bimodal cell population distributions with high and low target expression states, or correlated fluctuations across targets when the pool of unbound targets and miRNAs are in near-equimolar concentration. We found that there is an optimal range of conditions for the onset of cross-regulation, which is compatible with 10-1000 copies of targets per cell. Our results are summarized in a phase diagram for miRNA-mediated cross-regulation that links experimentally measured quantities and effective model parameters. This phase diagram can be applied to in vivo studies of RNAs that are in competition for miRNA binding.", "MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.", "Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA (mtDNA) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition/transversion ratio for the entire control region was approximately 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000-480,000 years in humans and 0.57-2.72 Myr in common chimpanzees.", "Recent studies have reported that competitive endogenous RNAs (ceRNAs) can act as sponges for a microRNA (miRNA) through their binding sites and that changes in ceRNA abundances from individual genes can modulate the activity of miRNAs. Consideration of this hypothesis would benefit from knowing the quantitative relationship between a miRNA and its endogenous target sites. Here, we altered intracellular target site abundance through expression of an miR-122 target in hepatocytes and livers and analyzed the effects on miR-122 target genes. Target repression was released in a threshold-like manner at high target site abundance (≥1.5 × 10(5) added target sites per cell), and this threshold was insensitive to the effective levels of the miRNA. Furthermore, in response to extreme metabolic liver disease models, global target site abundance of hepatocytes did not change sufficiently to affect miRNA-mediated repression. Thus, modulation of miRNA target abundance is unlikely to cause significant effects on gene expression and metabolism through a ceRNA effect.", "Here, we demonstrate that protein-coding RNA transcripts can crosstalk by competing for common microRNAs, with microRNA response elements as the foundation of this interaction. We have termed such RNA transcripts as competing endogenous RNAs (ceRNAs). We tested this hypothesis in the context of PTEN, a key tumor suppressor whose abundance determines critical outcomes in tumorigenesis. By a combined computational and experimental approach, we identified and validated endogenous protein-coding transcripts that regulate PTEN, antagonize PI3K/AKT signaling, and possess growth- and tumor-suppressive properties. Notably, we also show that these genes display concordant expression patterns with PTEN and copy number loss in cancers. Our study presents a road map for the prediction and validation of ceRNA activity and networks and thus imparts a trans-regulatory function to protein-coding mRNAs.", "Patients with estrogen receptor α (ERα)-positive breast cancer can be treated with endocrine therapy using anti-estrogens such as tamoxifen; nonetheless, patients often develop resistance limiting the success of breast cancer treatment. The potential mechanisms remain elusive. In detail, many miRNAs have been associated with breast cancer tamoxifen resistance, but no studies have addressed the role of miRNA-mediated competitive endogenous RNAs network (ceRNET) in tamoxifen resistance. The ceRNET between CYP4Z1 and pseudogene CYP4Z2P has been revealed to promote breast cancer angiogenesis. However, its function in tamoxifen resistance remains unclear. Here we report CYP4Z1 and CYP4Z2P were downregulated in MCF-7 cells compared with tamoxifen-resistant MCF-7-TamR cells. Enforced upregulation of CYP4Z1- or CYP4Z2P-3'UTR level renders MCF-7 Cells resistant to tamoxifen. We find that overexpression of CYP4Z1- or CYP4Z2P-3'UTR enhances the transcriptional activity of ERα through the activation of ERα phosphorylation. Furthermore, we find that CYP4Z1- and CYP4Z2P-3'UTRs increase ERα activity dependent on cyclin-dependent kinase 3 (CDK3). Reporter gene and western blot assays revealed that CYP4Z1- and CYP4Z2P-3'UTRs act as CDK3 ceRNAs. More importantly, the blocking of CYP4Z1- and CYP4Z2P-3'UTRs reversed tamoxifen resistance in MCF-7-TamR cells. Our data demonstrates that the ceRNET between CYP4Z1 and pseudogene CYP4Z2P acts as a sub-ceRNET to promote CDK3 expression in ER-positive breast cancer and is a potential therapeutic target for treatment of tamoxifen-resistant breast cancer.", "We present a statistical model of genes in DNA. A Generalized Hidden Markov Model (GHMM) provides the framework for describing the grammar of a legal parse of a DNA sequence (Stormo & Haussler 1994). Probabilities are assigned to transitions between states in the GHMM and to the generation of each nucleotide base given a particular state. Machine learning techniques are applied to optimize these probabilities using a standardized training set. Given a new candidate sequence, the best parse is deduced from the model using a dynamic programming algorithm to identify the path through the model with maximum probability. The GHMM is flexible and modular, so new sensors and additional states can be inserted easily. In addition, it provides simple solutions for integrating cardinality constraints, reading frame constraints, \"indels\", and homology searching. The description and results of an implementation of such a gene-finding model, called Genie, is presented. The exon sensor is a codon frequency model conditioned on windowed nucleotide frequency and the preceding codon. Two neural networks are used, as in (Brunak, Engelbrecht, & Knudsen 1991), for splice site prediction. We show that this simple model performs quite well. For a cross-validated standard test set of 304 genes [ftp:@www-hgc.lbl.gov/pub/genesets] in human DNA, our gene-finding system identified up to 85% of protein-coding bases correctly with a specificity of 80%. 58% of exons were exactly identified with a specificity of 51%. Genie is shown to perform favorably compared with several other gene-finding systems." ]
Ser 422 is required for IRS-1 degradation induced by prolonged IGF stimulation	The insulin receptor substrate IRS-1 is a key substrate of insulin and insulin-like growth factor (IGF) receptor tyrosine kinases that mediates their metabolic and growth-promoting actions. Proteasomal degradation of IRS-1 is induced following activation of the downstream kinase mTOR complex 1 (mTORC1) to constitute a negative feedback loop. However, the underlying mechanism remains poorly understood. Here we report that Ser 422 of IRS-1 is phosphorylated by mTORC1 and required for IRS-1 degradation induced by prolonged IGF stimulation. Phosphorylation of Ser 422 then recruits the SCF	[ "Inflammation associates with peripheral insulin resistance, which dysregulates nutrient homeostasis and leads to diabetes. Inflammation induces the expression of SOCS proteins. We show that SOCS1 or SOCS3 targeted IRS1 and IRS2, two critical signaling molecules for insulin action, for ubiquitin-mediated degradation. SOCS1 or SOCS3 bound both recombinant and endogenous IRS1 and IRS2 and promoted their ubiquitination and subsequent degradation in multiple cell types. Mutations in the conserved SOCS box of SOCS1 abrogated its interaction with the elongin BC ubiquitin-ligase complex without affecting its binding to IRS1 or IRS2. The SOCS1 mutants also failed to promote the ubiquitination and degradation of either IRS1 or IRS2. Adenoviral-mediated expression of SOCS1 in mouse liver dramatically reduced hepatic IRS1 and IRS2 protein levels and caused glucose intolerance; by contrast, expression of the SOCS1 mutants had no effect. Thus, SOCS-mediated degradation of IRS proteins, presumably via the elongin BC ubiquitin-ligase, might be a general mechanism of inflammation-induced insulin resistance, providing a target for therapy.", "Tuberous sclerosis (TSC) is an autosomal dominant disorder characterized by the formation of hamartomas in a wide range of human tissues. Mutation in either the TSC1 or TSC2 tumour suppressor gene is responsible for both the familial and sporadic forms of this disease. TSC1 and TSC2 proteins form a physical and functional complex in vivo. Here, we show that TSC1-TSC2 inhibits the p70 ribosomal protein S6 kinase 1 (an activator of translation) and activates the eukaryotic initiation factor 4E binding protein 1 (4E-BP1, an inhibitor of translational initiation). These functions of TSC1-TSC2 are mediated by inhibition of the mammalian target of rapamycin (mTOR). Furthermore, TSC2 is directly phosphorylated by Akt, which is involved in stimulating cell growth and is activated by growth stimulating signals, such as insulin. TSC2 is inactivated by Akt-dependent phosphorylation, which destabilizes TSC2 and disrupts its interaction with TSC1. Our data indicate a molecular mechanism for TSC2 in insulin signalling, tumour suppressor functions and in the inhibition of cell growth.", "In recent years, members of the protein kinase family have been discovered at an accelerated pace. Most were first described, not through the traditional biochemical approach of protein purification and enzyme assay, but as putative protein kinase amino acid sequences deduced from the nucleotide sequences of molecularly cloned genes or complementary DNAs. Phylogenetic mapping of the conserved protein kinase catalytic domains can serve as a useful first step in the functional characterization of these newly identified family members.", "Insulin receptor substrates-1 and 2 (IRS-1 and IRS-2) are pivotal in relaying insulin signaling in insulin-responsive tissues such as muscle. However, the precise contribution of IRS-1 vis-a-vis IRS-2 in insulin-mediated metabolic and mitogenic responses has not been compared directly in differentiated muscle cells. This study aimed to determine the relative contribution of IRS-1 versus IRS-2 in these responses, using small interfering RNA (siRNA)-mediated specific gene silencing. In L6 myotubes, transfection of siRNA targeted specifically against IRS-1 (siIRS-1) or IRS-2 (siIRS-2) reduced the cognate protein expression by 70-75%. Insulin-induced ERK phosphorylation was much more sensitive to IRS-2 than IRS-1 ablation, whereas p38MAPK phosphorylation was reduced by 43 or 62% in myotubes treated with siIRS-1 or siIRS-2, respectively. Insulin-induced Akt1 and Akt2 phosphorylation was reduced in myotubes treated with siIRS-1, but only Akt2 phosphorylation was reduced in myotubes treated with siIRS-2. In contrast, siIRS-1 treatment caused a marked reduction in insulin-induced actin remodeling, glucose uptake, and GLUT4 translocation, and siIRS-2 was without effect on these responses. Notably, combined siIRS-1 and siIRS-2, although reducing each IRS by around 75%, caused no further drop in glucose uptake than that achieved with siIRS-1 alone, but abolished p38MAPK phosphorylation. We conclude that insulin-stimulated Akt1 phosphorylation, actin remodeling, GLUT4 translocation, and glucose uptake are regulated mainly by IRS-1, whereas IRS-2 contributes selectively to ERK signaling, and Akt2 and p38MAPK lie downstream of both IRS in muscle cells.", "IRS-1 (insulin receptor substrate 1) is a principal insulin receptor substrate that undergoes tyrosine phosphorylation during insulin stimulation. It contains over 20 potential tyrosine phosphorylation sites, and we suspect that multiple insulin signals are enabled when the activated insulin receptor kinase phosphorylates several of them. Tyrosine-phosphorylated IRS-1 binds specifically to various cellular proteins containing Src homology 2 (SH2) domains (SH2 proteins). We identified some of the tyrosine residues of IRS-1 that undergo insulin-stimulated phosphorylation by the purified insulin receptor and in intact cells during insulin stimulation. Automated sequencing and manual radiosequencing revealed the phosphorylation of tyrosine residues 460, 608, 628, 895, 939, 987, 1172, and 1222; additional sites remain to be identified. Immobilized SH2 domains from the 85-kDa regulatory subunit (p85 alpha) of the phosphatidylinositol 3'-kinase bind preferentially to tryptic phosphopeptides containing Tyr(P)-608 and Tyr(P)-939. By contrast, the SH2 domain in GRB2 and the amino-terminal SH2 domain in SHPTP2 (Syp) specifically bind to Tyr(P)-895 and Tyr(P)-1172, respectively. These results confirm the p85 alpha recognizes YMXM motifs and suggest that GRB2 prefers a phosphorylated YVNI motif, whereas SHPTP2 (Syp) binds to a phosphorylated YIDL motif. These results extend the notion that IRS-1 is a multisite docking protein that engages various downstream regulatory elements during insulin signal transmission.", "Phospholipase C gamma 1 (PLC gamma 1) and p21ras guanosine triphosphatase (GTPase) activating protein (GAP) bind to and are phosphorylated by activated growth factor receptors. Both PLC gamma 1 and GAP contain two adjacent copies of the noncatalytic Src homology 2 (SH2) domain. The SH2 domains of PLC gamma 1 synthesized individually in bacteria formed high affinity complexes with the epidermal growth factor (EGF)- or platelet derived growth factor (PDGF)-receptors in cell lysates, and bound synergistically to activated receptors when expressed together as one bacterial protein. In vitro complex formation was dependent on prior growth factor stimulation and was competed by intracellular PLC gamma 1. Similar results were obtained for binding of GAP SH2 domains to the PDGF-receptor. The isolated SH2 domains of other signaling proteins, such as p60src and Crk, also bound activated PDGF-receptors in vitro. SH2 domains, therefore, provide a common mechanism by which enzymatically diverse regulatory proteins can physically associate with the same activated receptors and thereby couple growth factor stimulation to intracellular signal transduction pathways." ]
Classification of ENTorhinal Cortex Gray Matter in Patients with Temporal Lobe Epilepsy	Evidence for structural connectivity patterns within the medial temporal lobe derives primarily from postmortem histological studies. In humans and nonhuman primates, the parahippocampal gyrus (PHg) is subdivided into parahippocampal (PHc) and perirhinal (PRc) cortices, which receive input from distinct cortical networks. Likewise, their efferent projections to the entorhinal cortex (ERc) are distinct. The PHc projects primarily to the medial ERc (M-ERc). The PRc projects primarily to the lateral portion of the ERc (L-ERc). Both M-ERc and L-ERc, via the perforant pathway, project to the dentate gyrus and hippocampal (HC) subfields. Until recently, these neural circuits could not be visualized in vivo. Diffusion tensor imaging algorithms have been developed to segment gray matter structures based on probabilistic connectivity patterns. However, these algorithms have not yet been applied to investigate connectivity in the temporal lobe or changes in connectivity architecture related to disease processes. In this study, this segmentation procedure was used to classify ERc gray matter based on PRc, ERc, and HC connectivity patterns in 7 patients with temporal lobe epilepsy (TLE) without hippocampal sclerosis (mean age, 14.86 ± 3.34 years) and 7 healthy controls (mean age, 23.86 ± 2.97 years). Within samples paired t-tests allowed for comparison of ERc connectivity between epileptogenic and contralateral hemispheres. In healthy controls, there were no significant within-group differences in surface area, volume, or cluster number of ERc connectivity-defined regions (CDR). Likewise, in line with histology results, ERc CDR in the control group were well-organized, uniform, and segregated via PRc/PHc afferent and HC efferent connections. Conversely, in TLE, there were significantly more PRc and HC CDR clusters in the epileptogenic than the contralateral hemisphere. The surface area of the PRc CDR was greater, and that of the HC CDRs was smaller, in the epileptogenic hemisphere as well. Further, there was no clear delineation between M-ERc and L-ERc connectivity with PRc, PHc or HC in TLE. These results suggest a breakdown of the spatial organization of PHg-ERc-HC connectivity in TLE. Whether this breakdown is the cause or result of epileptic activity remains an exciting research question.	[ "To assess the quantitative diffusion characteristics of the hippocampus with high-resolution diffusion tensor imaging (DTI) in temporal lobe epilepsy (TLE). Thirteen controls and seven unilateral TLE patients (six with hippocampal sclerosis, one with normal magnetic resonance imaging (MRI)) were scanned with DTI using a zonally magnified oblique multislice echo planar imaging (ZOOM-EPI) acquisition. Fractional anisotropy (FA) and mean diffusivity (MD) were measured in the hippocampi. The mean hippocampal MD ipsilateral to the seizure focus was higher than the contralateral MD in patients (p<0.05) and the mean MD in controls (p<0.001). Hippocampal FA ipsilateral to the seizure focus was lower than the mean FA in controls (p<0.05). MD asymmetry indexes were significantly different between the patient and control groups (p<0.01). All six individual HS patients had ipsilateral hippocampal MD >or=2 standard deviations (S.D.) above the control mean. The patient with normal structural MRI had bilaterally low hippocampal FA and high MD. High-resolution DTI identifies lateralizing abnormalities of MD and FA in TLE patients. This quantitative data on hippocampal integrity may assist in evaluating TLE patients with normal MRI, and in longitudinal studies.", "This study used magnetic resonance spectroscopy (MRS) to examine metabolite abnormalities in the temporal and frontal lobe of patients with temporal lobe epilepsy (TLE) of differing severity. We investigated myoinositol in TLE by using short-echo MRS in 34 TLE patients [26 late onset (LO-TLE), eight hippocampal sclerosis (HS-TLE)], and 16 controls. Single-voxel short-echo (35 ms) MR spectra of temporal and frontal lobes were acquired at 1.5 T and analyzed by using LCModel. The temporal lobe ipsilateral to seizure origin in HS-TLE, but not LO-TLE, had reduced N-acetylaspartate (NA) and elevated myoinositol (MI; HS-TLE NA, 7.8 +/- 1.9 mM, control NA, 9.2 +/- 1.3 mM; p < 0.05; HS-TLE MI, 6.1 +/- 1.6 mM, control mI 4.9 +/- 0.8 mM, p< 0.05). Frontal lobe MI was low in both patient groups (LO-TLE, 4.3 +/- 0.8 mM; p < 0.05; HS-TLE, 3.6 +/-.05 mM; p < 0.001; controls, 4.8 +/- 0.5 mM). Ipsilateral frontal lobes had lower MI (3.8 +/- 0.7 mM; p < 0.01) than contralateral frontal lobes (4.3 +/- 0.8 mM; p < 0.05). MI changes may distinguish between the seizure focus, where MI is increased, and areas of seizure spread where MI is decreased.", "Patients with temporal lobe epilepsy display neuron loss in the hilus of the dentate gyrus. This has been proposed to be epileptogenic by a variety of different mechanisms. The present study examines the specificity and extent of neuron loss in the dentate gyrus of kainate-treated rats, a model of temporal lobe epilepsy. Kainate-treated rats lose an average of 52% of their GAD-negative hilar neurons (putative mossy cells) and 13% of their GAD-positive cells (GABAergic interneurons) in the dentate gyrus. Interneuron loss is remarkably specific; 83% of the missing GAD-positive neurons are somatostatin-immunoreactive. Of the total neuron loss in the hilus, 97% is attributed to two cell types-mossy cells and somatostatinergic interneurons. The retrograde tracer wheat germ agglutinin (WGA)-apoHRP-gold was used to identify neurons with appropriate axon projections for generating lateral inhibition. Previously, it was shown that lateral inhibition between regions separated by 1 mm persists in the dentate gyrus of kainate-treated rats with hilar neuron loss. Retrogradely labeled GABAergic interneurons are found consistently in sections extending 1 mm septotemporally from the tracer injection site in control and kainate-treated rats. Retrogradely labeled putative mossy cells are found up to 4 mm from the injection site, but kainate-treated rats have fewer than controls, and in several kainate-treated rats virtually all of these cells are missing. These findings support hypotheses of temporal lobe epileptogenesis that involve mossy cell and somatostatinergic neuron loss and suggest that lateral inhibition in the dentate gyrus does not require mossy cells but, instead, may be generated directly by GABAergic interneurons.", "The sulci and gyri found within the anterior cingulate (AC), and across the cerebrum generally, have been found to vary in location and complexity from one individual to the next, making it difficult to analyze imaging data accurately and systematically. In this study, we examined the nature of morphometric variance in the AC of the left and right cerebral hemispheres using high-resolution structural magnetic resonance imaging (MRI) acquired from 176 healthy volunteers. Depending on the presence of a paracingulate sulcus (PCS) and its antero-posterior extent, three types of AC patterns were identified: 'prominent', 'present' and 'absent'. Hemispheric comparisons across the whole sample showed the PCS to be more commonly 'prominent' in the left hemisphere and more commonly 'absent' in the right hemisphere. There was a significant gender difference, such that males showed an asymmetric pattern characterized by increased fissurization of the left AC, while females showed greater symmetry, with less fissurization of the left AC. Overall cerebral morphology, namely hemispheric volume and hemispheric fissurization, were also measured and used as independent variables as well as covariates in the analyses in order to ascertain the specificity of the results regarding AC morphology. Results showed that cerebral volume for males was larger on the right than on the left while fissurization showed the reverse asymmetry of greater leftward fissurization. In contrast, females were symmetric in both respects. The findings regarding AC morphology could not be explained by differences in these overall cerebral measures or by differences in age and handedness within the population. The results suggest that in the normal male brain, there exist morphological asymmetries at both the global and local levels that are less apparent in the female brain. The findings have implications for future studies examining the organization, development and functional anatomy of the AC.", "In a series of 40 patients undergoing an awake craniotomy for the removal of a glioma of the dominant hemisphere temporal lobe, cortical stimulation mapping was used to localize essential language sites. These sites were localized to distinct temporal lobe sectors and compared with 83 patients without tumors who had undergone language mapping for the treatment of intractable epilepsy. In patients with and without temporal lobe gliomas, the superior temporal gyrus contained significantly more language sites than the middle temporal gyrus. Both patient populations also had language sites anterior to the central sulcus in the superior temporal gyrus (12-16%). The patients without tumors had significantly more language sites in the superior temporal gyrus, compared with the superior temporal gyrus of patients with temporal lobe tumors. Multiple variables were studied for their effect on preoperative and postoperative language deficits and included age, sex, number of language sites, histology, size of the tumor, and the distance of tumor resection margins from the nearest language site. The distance of the resection margin from the nearest language site was the most important variable in determining the improvement in preoperative language deficits, the duration of postoperative language deficits, and whether the postoperative language deficits were permanent. If the distance of the resection margin from the nearest language site was > 1 cm, significantly fewer permanent language deficits occurred. Cortical stimulation mapping for the identification of essential language sites in patients with gliomas of the dominant hemisphere temporal lobe will maximize the extent of tumor resection and minimize permanent language deficits.", "Functional resting-state connectivity has been shown to be altered in certain adult epilepsy populations, but few connectivity studies have been performed on pediatric epilepsy patients. Here functional connectivity was measured in pediatric, non-lesional temporal lobe epilepsy patients with normal intelligence and compared with that in age and gender-matched healthy controls using the independent component analysis method. We hypothesized that children with non-lesional temporal lobe epilepsy have disrupted functional connectivity within resting-state networks. Significant differences were demonstrated between the two groups, pointing to a decrease in connectivity. When the results were analyzed according to the interictal electroencephalogram findings, however, the connectivity disruptions were seen in different networks. In addition, increased connectivity and abnormally anti-correlated thalamic activity was detected only in the patients with abnormal electroencephalograms. In summary, connectivity disruptions are already to be seen at an early stage of epilepsy, and epileptiform activity seems to affect connectivity differently. The results indicate that interictal epileptiform activity may lead to reorganization of the resting-state brain networks, but further studies would be needed in order to understand the pathophysiology behind this phenomenon.", "One challenge in dominant hemisphere epilepsy surgery is to remove sufficient epileptogenic tissue to achieve seizure freedom without compromising postoperative language function. Electrical stimulation mapping (ESM) of language was developed specifically to identify essential language cortex in pharmacologically intractable epilepsy patients undergoing left hemisphere resection of epileptogenic cortex. Surprisingly, the procedure remains unstandardized, and limited data support its clinical validity. Nevertheless, ESM for language mapping has likely minimized postoperative language decline in numerous patients, and has generated a wealth of data elucidating brain-language relations. This article reviews the literature on topographical patterns of language organization inferred from ESM, and the influence of patient characteristics on these patterns, including baseline ability level, age, gender, pathology, degree of language lateralization and bilingualism. Questions regarding clinical validity and limitations of ESM are discussed. Finally, recommendations for clinical practice are presented, and theoretical questions regarding ESM and the findings it has generated are considered." ]
Co-occurring patterns of 3,4-Methylenedioxymethamphetamine use and injection drug use among street-involved youth	Childhood trauma is common among street-involved youth and is associated with injection drug use. Illicit 3,4-Methylenedioxymethamphetamine (MDMA) use is also common among street-involved youth, and data suggest this substance has clinical utility in management of post-traumatic stress disorder (PTSD) and associated harms. Despite this, little is known about co-occurring patterns of MDMA use and injection drug use.	[ "Both recreational and problematic MDMA/ecstasy users could benefit from employing harm reduction interventions intended to preserve health and prevent negative consequences. To evaluate whether use of such interventions varied by country of residence and frequency of ecstasy use, we used web-based surveys to assess how often 104 lower-frequency and higher-frequency American ecstasy users and 80 lower-frequency and higher-frequency British ecstasy users employed each of 19 self-initiated harm reduction strategies when they used ecstasy during a two-month period. Several significant differences notwithstanding, at least 75% of participants had used 11 of the 19 strategies one or more times during the two-month assessment period, regardless of whether they lived in the United States or United Kingdom and whether they were lower-frequency or higher-frequency ecstasy users. When proportions of American and British participants using a strategy differed significantly, it was typically larger proportions of Americans using those strategies. Many of the less frequently employed strategies are not applicable on every occasion of ecstasy use. However, because ecstasy is not a diverted pharmaceutical of known quality/potency, testing for the presence of MDMA, other stimulants, and adulterants is a strategy that everyone should employ, regardless of country of residence or how frequently one consumes ecstasy.", "We examined associations between childhood trauma and adulthood prescription pain reliever misuse (PPRM) and injection drug use (IDU) in a nationally-representative U.S. sample to further understanding of factors associated with these epidemics. National Longitudinal Study of Adolescent to Adult Health data (N=12,288) yielded nine childhood traumas: neglect; emotional, physical, sexual abuse; parental incarceration and binge drinking; witnessed, threatened with, and experienced violence. We estimated adjusted odds ratios (AOR) and 95% confidence intervals for the association of each trauma and cumulative trauma and drug initiation in emerging and later adulthood. Outcome prevalences were 20% (PPRM) and 1% (IDU) in emerging adulthood and 10% PPRM in adulthood. We observed dose-response relationships that varied across outcomes. Cumulative trauma (referent=none) was associated with 34-79% greater odds of PPRM (emerging adulthood) across one to five+ trauma categories. The gradient was most consistent and associations strongest for adulthood PPRM: one trauma AOR=1.46(1.12, 1.91); two AOR=1.71(1.23, 2.36); three AOR=2.16(1.43, 2.36); four AOR=2.70(1.42, 5.62); five+ AOR=3.09(1.52, 6.30). Dose-response was less consistent for IDU, but 4 and 5+ traumas were associated with approximately seven and five times the odds of IDU. Neglect, emotional abuse, and parental incarceration and binge drinking were associated with 25-55% increased odds of PPRM. Sexual abuse and witnessed violence were associated with nearly 3 and 5 times the odds of IDU. Associations between childhood trauma and PPRM/IDU highlight the need for trauma-informed interventions for drug users and early trauma screening and treatment for prevention of drug misuse over the life course.", "The present study examined the developmental antecedents of illicit drug use and abuse/dependence. A 25-year prospective longitudinal study of the health, development, and adjustment of a birth cohort of 1265 New Zealand children. Measures included assessments of adolescent and young adult illicit drug use and abuse/dependence; cannabis use to age 25; measures of parental adjustment; measures of exposure to childhood sexual abuse, physical abuse, and interparental violence; novelty-seeking; childhood and early adolescent adjustment and substance use; and affiliation with substance-using peers. Illicit drug use and abuse/dependence from ages 16 to 25 were significantly associated (all p values<.05) with a range of parental adjustment measures; exposure to abuse in childhood; individual factors; and measures of childhood and early adolescent adjustment. Analyses using repeated measures logistic regression models suggested that parental illicit drug use, gender, novelty-seeking, and childhood conduct disorder predicted later illicit drug use and abuse/dependence. Further analyses revealed that these pathways to illicit drug use and abuse/dependence were mediated via cannabis use, affiliation with substance-using peers, and alcohol use during ages 16-25. The current study suggested that the illicit drug use and abuse/dependence were associated with a range of early life circumstances and processes that put individuals at greater risk of illicit drug use and abuse/dependence. However, the use of cannabis in late adolescence and early adulthood emerged as the strongest risk factor for later involvement in other illicit drugs.", "This study examined the association between age at alcohol use onset and adult alcohol misuse and dependence by testing the sensitive-period hypothesis that early adolescence (11-14) is a vulnerable period of development during which initiating alcohol use is particularly harmful. Data came from a longitudinal panel of 808 participants recruited in 1981. Participants were followed through age 33 in 2008 with 92% retention. Onset of alcohol use before age 11 (late childhood), when compared with initiation during early adolescence, was related to an increased chronicity of adult alcohol dependence, even after accounting for sociodemographic controls and other substance use in adolescence. The present study finds no evidence that early adolescence is a particularly sensitive period for the onset of alcohol use. Findings related to the onset of regular alcohol use and the chronicity of alcohol dependence suggest that the onset of regular drinking before age 21 is problematic, but no one adolescent period is more sensitive than others. Specifically, although all age groups that started drinking regularly before age 21 had a greater rate of alcohol dependence in adulthood, initiation of regular use of alcohol at or before age 14 was not related to greater chronicity of alcohol dependence than the initiation of regular use of alcohol in middle or late adolescence. The findings suggest the importance of delaying the onset of alcohol use through prevention efforts as early as the elementary grades. In addition, prevention efforts should focus on preventing the onset of regular drinking before age 21.", "This study compared male and female injection drug users (IDUs) on perceived risk of contracting HIV and examined the associations between risk perceptions and sharing injection drugs or equipment, engaging in casual sex, and engaging in commercial sex. We used baseline data from 271 IDUs recruited between 2000 and 2005 from the Baltimore, Maryland site of the International Neurobehavioral HIV Study. We found that although there was no significant difference in levels of perceived risk between males and females, males reported significantly more casual sex, whereas females reported more commercial sex. Logistic regression analyses with the entire sample indicated that sharing of injection drugs or equipment was consistently associated with greater perceived risk. We also found a significant interaction between gender and having had casual sex, such that females who had engaged in casual sex were significantly more likely to perceive that they were at greater risk for contracting HIV. Our results suggest that male IDUs should be targeted for HIV risk-reduction programs focusing on casual and commercial sex.", "Early onset of alcohol, marijuana, and cigarette use is an indicator of later substance use problems in adulthood such as alcohol or other drug dependence. This paper seeks to address the association between early onset alcohol, marijuana, cigarette, and polysubstance use with injection drug use among recent illicit drug users. The current study used baseline data from the Baltimore site of the NEURO-HIV Epidemiologic Study, an investigation of neuropsychological and social-behavioral risk factors of HIV, hepatitis A, hepatitis B, and Hepatitis C among both injection and non-injection drug users in Baltimore, Maryland. The present study used a subset (N=651) of the larger parent study that identified as White or Black, and reported any drug use in the past 6 months. In the full sample slightly more than half (52.5%) of study participants were IDUs. IDUs differed from non-IDUs on age of initiation for cigarettes, marijuana, and alcohol, with IDUs initiating the use of all three substances significantly earlier than non-IDUs. IDUs also had significantly greater proportions of early onset of alcohol (χ(2)=19.71, p<.01), cigarette (χ(2)=11.05, p<.01), marijuana (χ(2)=10.83, p<.01), and polysubstance use (χ(2)=23.48, p<.01) than non-IDUs. After adjusting for age, gender, and race/ethnicity, only participants identified as early onset alcohol users (AOR=1.47, 95% CI: 1.00-2.18) and early onset polysubstance users (AOR=1.62, 95% CI: 1.10-2.38) were more likely to have IDU status than those who reported initiating substance use later. IDU status was then stratified by race/ethnicity. After controlling for age and gender, only early polysubstance use was a significant predictor of IDU status for Whites (AOR=2.06, 95% CI: 1.07-3.93). Consistent with literature on early substance initiation and later illicit substance use, early onset of alcohol and polysubstance use is an important risk factor for IDU in adulthood.", "To review and synthesize the recent scientific literature on adolescent substance abuse, covering natural history, epidemiology, etiology, comorbidity, assessment, treatment, and prevention, and to highlight areas for future research. Studies of adolescent substance abuse were reviewed with the focus on substance abuse and dependence rather than substance use. There has been a sharp recent resurgence in adolescent drug use. Biological factors, including genetic and temperament characteristics, as well as family environment factors, are emerging as important etiological variables. Comorbidity with other psychiatric disorders, particularly with conduct disorder, is frequent and complicates treatment. New assessment instruments are available for clinical and research use. Among treatment modalities, family-based interventions have received the most study. The past decade has seen growth in the volume and sophistication of research on adolescent substance abuse and in the conceptualization of this problem. Further research is needed, particularly on the significance of comorbid conditions and on individualized and effective treatment approaches." ]
Kinematic Flexibility Analysis of Protein Motions	Elastic network models (ENMs) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have contributed significantly to insights into protein molecular mechanisms and function. However, despite a shared purpose of these approaches, the topological nature of rigidity analysis, and thereby the absence of motion modes, has impeded a direct comparison. Here, we present an alternative, kinematic approach to rigidity analysis, which circumvents these drawbacks. We introduce a novel protein hydrogen bond network spectral decomposition, which provides an orthonormal basis for collective motions modulated by noncovalent interactions, analogous to the eigenspectrum of normal modes. The zero modes decompose proteins into rigid clusters identical to those from topological rigidity, while nonzero modes rank protein motions by their hydrogen bond collective energy penalty. Our kinematic flexibility analysis bridges topological rigidity theory and ENM, enabling a detailed analysis of motion modes obtained from both approaches. Analysis of a large, structurally diverse data set revealed that collectivity of protein motions, reported by the Shannon entropy, is significantly reduced for rigidity theory compared to normal mode approaches. Strikingly, kinematic flexibility analysis suggests that the hydrogen bonding network encodes a protein-fold specific, spatial hierarchy of motions, which goes nearly undetected in ENM. This hierarchy reveals distinct motion regimes that rationalize experimental and simulated protein stiffness variations. Kinematic motion modes highly correlate with reported crystallographic B factors and molecular dynamics simulations of adenylate kinase. A formal expression for changes in free energy derived from the spectral decomposition indicates that motions across nearly 40% of modes obey enthalpy-entropy compensation. Taken together, our results suggest that hydrogen bond networks have evolved to modulate protein structure and dynamics, which can be efficiently probed by kinematic flexibility analysis.	[ "A new approach is presented for determining the rigid regions in proteins and the flexible joints between them. The short-range forces in proteins are modeled as constraints and we use a recently developed formalism from graph theory to analyze flexibility in the bond network. Forces included in the analysis are the covalent bond-stretching and bond-bending forces, salt bridges, and hydrogen bonds. We use a local function to associate an energy with individual hydrogen bonds, which then can be included or excluded depending on the bond strength. Colored maps of the rigid and flexible regions provide a direct visualization of where the motion of the protein can take place, consistent with these distance constraints. We also define a flexibility index that quantifies the local density of flexible or floppy modes, in terms of the dihedral angles that remain free to rotate in each flexible region. A negative flexibility index provides a measure of the density of redundant bonds in rigid regions. A new application of this approach is to simulate the maximal range of possible motions of the flexible regions by introducing Monte Carlo changes in the free dihedral angles, subject to the distance constraints. This is done using a method that maintains closure of the rings formed by covalent and hydrogen bonds in the flexible parts of the protein, and van der Waals overlaps between atoms are avoided. We use the locus of the possible motions of HIV protease as an example: movies of its motion can be seen at http://www.pa.msu.edu/~lei.", "There are 17 crystal structures of nucleoside monophosphate kinases known. As expected for kinases, they show large conformational changes upon binding of substrates. These are concentrated in two chain segments, or domains, of 30 and 38 residues that are involved in binding of the substrates N1TP and N2MP (nucleoside tri- and monophosphates with bases N1 and N2), respectively. After aligning the 17 structures on the main parts of their polypeptide chains, two domains in various conformational states were revealed. These states were caused by bound substrate (or analogues) and by crystal-packing forces, and ranged between a 'closed' conformation and a less well defined 'open' conformation. The structures were visually sorted yielding an approximately evenly spaced series of domain states that outlines the closing motions when the substrates bind. The packing forces in the crystals are weak, leaving the natural domain trajectories essentially intact. Packing is necessary, however, to produce stable intermediates. The ordered experimental structures were then recorded as still pictures of a movie and animated to represent the motions of the molecule during a catalytic cycle. The motions were smoothed out by adding interpolated structures to the observed ones. The resulting movies are available through the World Wide Web (http:@bio5.chemie.uni-freiburg.de/ak movie.html). Given the proliferating number of homologous proteins known to exist in different conformational states, it is becoming possible to outline the motions of chain segments and combine them into a movie, which can then represent protein action much more effectively than static pictures alone are able to do.", "The functional cycle of many proteins involves large-scale motions of domains and subunits. The relation between conformational dynamics and the chemical steps of enzymes remains under debate. Here we show that in the presence of substrates, domain motions of an enzyme can take place on the microsecond time scale, yet exert influence on the much-slower chemical step. We study the domain closure reaction of the enzyme adenylate kinase from Escherichia coli while in action (i.e., under turnover conditions), using single-molecule FRET spectroscopy. We find that substrate binding increases dramatically domain closing and opening times, making them as short as ∼15 and ∼45 µs, respectively. These large-scale conformational dynamics are likely the fastest measured to date, and are ∼100-200 times faster than the enzymatic turnover rate. Some active-site mutants are shown to fully or partially prevent the substrate-induced increase in domain closure times, while at the same time they also reduce enzymatic activity, establishing a clear connection between the two phenomena, despite their disparate time scales. Based on these surprising observations, we propose a paradigm for the mode of action of enzymes, in which numerous cycles of conformational rearrangement are required to find a mutual orientation of substrates that is optimal for the chemical reaction.", "Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing--in atomic detail--how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.", "The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.", "There are 20(200) possible amino-acid sequences for a 200-residue protein, of which the natural evolutionary process has sampled only an infinitesimal subset. De novo protein design explores the full sequence space, guided by the physical principles that underlie protein folding. Computational methodology has advanced to the point that a wide range of structures can be designed from scratch with atomic-level accuracy. Almost all protein engineering so far has involved the modification of naturally occurring proteins; it should now be possible to design new functional proteins from the ground up to tackle current challenges in biomedicine and nanotechnology.", "Collagen type I is the most abundant structural protein in tendon, skin and bone, and largely determines the mechanical behaviour of these connective tissues. To obtain a better understanding of the relationship between structure and mechanical properties, tensile tests and synchrotron X-ray scattering have been carried out simultaneously, correlating the mechanical behaviour with changes in the microstructure. Because intermolecular cross-links are thought to have a great influence on the mechanical behaviour of collagen, we also carried out experiments using cross-link-deficient tail-tendon collagen from rats fed with beta-APN, in addition to normal controls. The load-elongation curve of tendon collagen has a characteristic shape with, initially, an increasing slope, corresponding to an increasing stiffness, followed by yielding and then fracture. Cross-link-deficient collagen produces a quite different curve with a marked plateau appearing in some cases, where the length of the tendon increases at constant stress. With the use of in situ X-ray diffraction, it was possible to measure simultaneously the elongation of the collagen fibrils inside the tendon and of the tendon as a whole. The overall strain of the tendon was always larger than the strain in the individual fibrils, which demonstrates that some deformation is taking place in the matrix between fibrils. Moreover, the ratio of fibril strain to tendon strain was dependent on the applied strain rate. When the speed of deformation was increased, this ratio increased in normal collagen but generally decreased in cross-link-deficient collagen, correlating to the appearance of a plateau in the force-elongation curve indicating creep. We proposed a simple structural model, which describes the tendon at a hierarchical level, where fibrils and interfibrillar matrix act as coupled viscoelastic systems. All qualitative features of the strain-rate dependence of both normal and cross-link-deficient collagen can be reproduced within this model. This complements earlier models that considered the next smallest level of hierarchy, describing the deformation of collagen fibrils in terms of changes in their molecular packing." ]
Molecular markers for mammalian axon growth and regeneration	Neuronal growth cones are essential for nerve growth and regeneration, as well as for the formation and rearrangement of the neural network. To elucidate phosphorylation-dependent signaling pathways and establish useful molecular markers for axon growth and regeneration, we performed a phosphoproteomics study of mammalian growth cones, which identified >30,000 phosphopeptides of ∼1,200 proteins. The phosphorylation sites were highly proline directed and primarily MAPK dependent, owing to the activation of JNK, suggesting that proteins that undergo proline-directed phosphorylation mediate nerve growth in the mammalian brain. Bioinformatics analysis revealed that phosphoproteins were enriched in microtubules and the cortical cytoskeleton. The most frequently phosphorylated site was S96 of GAP-43 (growth-associated protein 43-kDa), a vertebrate-specific protein involved in axon growth. This previously uncharacterized phosphorylation site was JNK dependent. S96 phosphorylation was specifically detected in growing and regenerating axons as the most frequent target of JNK signaling; thus it represents a promising new molecular marker for mammalian axonal growth and regeneration.	[ "c-Jun N-terminal kinase (JNK) signaling is an important contributor to stress-induced apoptosis, but it is unclear whether JNK and its isoforms (JNK1, JNK2, and JNK3) have distinct roles in cerebral ischemia. Here we show that JNK1 is the major isoform responsible for the high level of basal JNK activity in the brain. In contrast, targeted deletion of Jnk3 not only reduces the stress-induced JNK activity, but also protects mice from brain injury after cerebral ischemia-hypoxia. The downstream mechanism of JNK3-mediated apoptosis may include the induction of Bim and Fas and the mitochondrial release of cytochrome c. These results suggest that JNK3 is a potential target for neuroprotection therapies in stroke.", "β-Blockers are widely used to prevent cardiac arrhythmias and to treat hypertension by inhibiting β-adrenergic receptors (βARs) and thus decreasing contractility and heart rate. βARs initiate phosphorylation-dependent signaling cascades, but only a small number of the target proteins are known. We used quantitative in vivo phosphoproteomics to identify 670 site-specific phosphorylation changes in murine hearts in response to acute treatment with specific βAR agonists. The residues adjacent to the regulated phosphorylation sites exhibited a sequence-specific preference (R-X-X-pS/T), and integrative analysis of sequence motifs and interaction networks suggested that the kinases AMPK (adenosine 5'-monophosphate-activated protein kinase), Akt, and mTOR (mammalian target of rapamycin) mediate βAR signaling, in addition to the well-established pathways mediated by PKA (cyclic adenosine monophosphate-dependent protein kinase) and CaMKII (calcium/calmodulin-dependent protein kinase type II). We found specific regulation of phosphorylation sites on six ion channels and transporters that mediate increased ion fluxes at higher heart rates, and we showed that phosphorylation of one of these, Ser(92) of the potassium channel KV7.1, increased current amplitude. Our data set represents a quantitative analysis of phosphorylated proteins regulated in vivo upon stimulation of seven-transmembrane receptors, and our findings reveal previously unknown phosphorylation sites that regulate myocardial contractility, suggesting new potential targets for the treatment of heart disease and hypertension.", "c-Jun N-terminal kinase (JNK) is a member of the mitogen-activated protein kinase family and controls various physiological processes including apoptosis. A specific upstream activator of JNKs is the mitogen-activated protein kinase kinase 7 (MKK7). It has been reported that MKK7-JNK signaling plays an important regulatory role in neural development, however, post-developmental functions in the nervous system have not been elucidated. In this study, we generated neuron-specific Mkk7 knockout mice (MKK7 cKO), which impaired constitutive activation of JNK in the nervous system. MKK7 cKO mice displayed impaired circadian behavioral rhythms and decreased locomotor activity. MKK7 cKO mice at 8 months showed motor dysfunctions such as weakness of hind-limb and gait abnormality in an age-dependent manner. Axonal degeneration in the spinal cord and muscle atrophy were also observed, along with accumulation of the axonal transport proteins JNK-interacting protein 1 and amyloid beta precursor protein in the brains and spinal cords of MKK7 cKO mice. Thus, the MKK7-JNK signaling pathway plays important roles in regulating circadian rhythms and neuronal maintenance in the adult nervous system.", "c-Jun is considered a major regulator of both neuronal death and regeneration. Stress in primary cultured CNS neurons induces phosphorylation of c-Jun serines 63 and 73 and increased c-Jun protein. However, total c-Jun N-terminal protein kinase (JNK) activity does not increase, and no satisfactory explanation for this paradox has been available. Here we demonstrate that neuronal stress induces strong activation of JNK2/3 in the presence of constitutively and highly active JNK1. Correspondingly, neurons from JNK1(-/-) mice show lower constitutive activity and considerably higher responsiveness to stress. p38 activity can be completely inhibited without effect on c-Jun phosphorylation, whereas 10 micrometer SB203580 strongly inhibits neuronal JNK2/3, stress-induced c-Jun phosphorylation, induced c-Jun activity, and neuronal death in response to trophic withdrawal stress. Neither constitutive JNK1 activity nor total neuronal JNK activity were significantly affected by this concentration of drug. Thus, neuronal stress selectively activates JNK2/3 in the presence of mechanisms maintaining constitutive JNK1 activity, and this JNK2/3 activity selectively targets c-Jun, which is isolated from constitutive JNK1 activity.", "GAP-43 is an intracellular growth-associated protein that appears to assist neuronal pathfinding and branching during development and regeneration, and may contribute to presynaptic membrane changes in the adult, leading to the phenomena of neurotransmitter release, endocytosis and synaptic vesicle recycling, long-term potentiation, spatial memory formation, and learning. GAP-43 becomes bound via palmitoylation and the presence of three basic residues to membranes of the early secretory pathway. It is then sorted onto vesicles at the late secretory pathway for fast axonal transport to the growth cone or presynaptic plasma membrane. The palmitate chains do not serve as permanent membrane anchors for GAP-43, because at steady-state most of the GAP-43 in a cell is membrane-bound but is not palmitoylated. Filopodial extension and branching take place when GAP-43 is phosphorylated at Ser-41 by protein kinase C, and this occurs following neurotrophin binding and the activation of numerous small GTPases. GAP-43 has been proposed to cluster the acidic phospholipid phosphatidylinositol 4,5-bisphosphate in plasma membrane rafts. Following GAP-43 phosphorylation, this phospholipid is released to promote local actin filament-membrane attachment. The phosphorylation also releases GAP-43 from calmodulin. The released GAP-43 may then act as a lateral stabilizer of actin filaments. N-terminal fragments of GAP-43, containing 10-20 amino acids, will activate heterotrimeric G proteins, direct GAP-43 to the membrane and lipid rafts, and cause the formation of filopodia, possibly by causing a change in membrane tension. This review will focus on new information regarding GAP-43, including its binding to membranes and its incorporation into lipid rafts, its mechanism of action, and how it affects and is affected by extracellular agents.", "A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/.", "Activation of caspase-3 requires proteolytic processing of the inactive zymogen into p18 and p12 subunits. We generated a rabbit polyclonal antiserum, CM1, which recognizes the p18 subunit of cleaved caspase-3 but not the zymogen. CM1 demonstrated an apparent specificity for activated caspase-3 by specifically immunolabelling only apoptotic but not necrotic cortical neurons in vitro. In the embryonic mouse nervous system, CM1 immunoreactivity was detected in neurons undergoing programmed cell death and was markedly increased in Bcl-xL-deficient embryos and decreased in Bax-deficient embryos. CM1 immunoreactivity was absent in the nervous system of caspase-3-deficient mouse embryos and in neurons cultured from caspase-3-deficient mice. Along with neuronal somata, extensive neuritic staining was seen in apoptotic neurons. These studies indicate that caspase-3 is activated during apoptosis in the developing nervous system in vivo and that CM1 is a useful reagent for its in situ detection." ]
what is balamuthia mandrillaris	Balamuthia mandrillaris is a free-living ameba that causes rare, nearly always fatal disease in humans and animals worldwide. B. mandrillaris has been isolated from soil, dust, and water. Initial entry of Balamuthia into the body is likely via the skin or lungs. To date, only individual case reports and small case series have been published.	[ "Free-living amebae are ubiquitous in our environment, but rarely cause cutaneous infection. Balamuthia mandrillaris has a predilection for infecting skin of the central face. Infection may be restricted to the skin or associated with life-threatening central nervous system (CNS) involvement. We report a case of a 91-year-old woman, who presented with a non-healing red plaque over her right cheek. Several punch biopsies exhibited non-specific granulomatous inflammation without demonstrable fungi or mycobacteria in histochemical stains. She was treated empirically for granulomatous rosacea, but the lesion continued to progress. A larger incisional biopsy was performed in which amebae were observed in hematoxylin-eosin stained sections. These were retrospectively apparent in the prior punch biopsy specimens. Immunohistochemistry and polymerase chain reaction studies identified the organisms as Balamuthia mandrillaris. Cutaneous infection by B. mandrillaris is a rare condition that is sometimes complicated by life-threatening CNS involvement and which often evades timely diagnosis due to its rarity and nonspecific clinical manifestations. Moreover, these amebae are easily overlooked in histopathologic sections because of their small number and their resemblance to histiocytes. Dermatopathologists should be familiar with the histopathologic appearance of these organisms and include balamuthiasis and other amebic infections in the differential diagnosis of granulomatous dermatitis.", "Granulomatous amoebic encephalitis caused by Balamuthia mandrillaris is an uncommon infection for which there is no optimal therapy. We describe a young, female patient who presented with extensive cutaneous and neurological involvement and who recovered after receiving prolonged treatment with miltefosine, fluconazole, and albendazole.", "Balamuthia mandrillaris meningoencephalitis is a rare but often fatal infection; only 2 survivors have been reported to date worldwide. We report the case of an apparently immunocompetent patient (72-year-old woman) who developed several episodes of seizures without prior history of respiratory or skin infections. Magnetic resonance imaging with contrast revealed 2 ring-enhancing lesions, one in the right precentral region and the other in the left posterotemporal region. Open biopsy revealed Balamuthia encephalitis. The patient was treated with combination antibiotics (pentamidine, 300 mg intravenously once a day; sulfadiazine, 1.5 g 4 times a day; fluconazole, 400 mg once a day; and clarithromycin, 500 mg 3 times a day) and was discharged home. There have been no significant neurological sequelae at this writing (6 months after biopsy). We present this case with unusual clinical course to raise awareness of this infectious disease, which may have a more favorable outcome if diagnosed and treated in its early states.", "Granulomatous amebic encephalitis is an uncommon central nervous system (CNS) infection, usually caused by Acanthamoeba spp., which generally occurs in immunocompromised individuals. Balamuthia mandrillaris is a recently described free-living ameba that occasionally causes fatal CNS disease. The infection might start from a minor, slowly progressive, skin ulceration that can be present for weeks to months before neurologic changes occur. The clinical and histologic presentation is easily confused with many other diseases. Accurate diagnosis requires an awareness of this unusual presentation of amebiasis and identification of the amebic trophozoites in tissue and culture. Special stains are helpful, but immunofluorescence assays or electron microscopy is required to identify the organism as B mandrillaris. We present a fatal case of granulomatous amebic encephalitis that began as a cutaneous infection in an immunocompetent host." ]
Developing a World Code Against Cancer	Overwhelmed by an abundance of often confusing, ambiguous, or apparently contradictory messages on disease prevention in today's multiple media streams, the general public would surely value authoritative, clear, and evidence-based instructions on how to actively contribute to the reduction of their cancer risk. The European Code Against Cancer is a set of 12 recommendations for individuals on how to reduce cancer risk. The Code carries the authority and reliability of expert scientists working under the coordination of the International Agency for Research on Cancer, the cancer research agency of the WHO. The Code's messages are aimed at individuals and have been enthusiastically promoted by European cancer associations. The experience of developing and promoting the European Code has generated interest in developing analogous recommendations for other regions of the world. Under the overall umbrella of a World Code Against Cancer using the same International Agency for Research on Cancer methodology, regional Codes could be developed, focused on regions sufficiently large and distinct to merit development of versions adapted to regional differences in risk factors and cancer patterns. Consideration of such an adapted model illustrates why a simple translation of the European Code would not be sufficient to promote cancer prevention globally.	[ "The scale-up of tobacco control, especially after the adoption of the Framework Convention for Tobacco Control, is a major public health success story. Nonetheless, smoking remains a leading risk for early death and disability worldwide, and therefore continues to require sustained political commitment. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) offers a robust platform through which global, regional, and national progress toward achieving smoking-related targets can be assessed. We synthesised 2818 data sources with spatiotemporal Gaussian process regression and produced estimates of daily smoking prevalence by sex, age group, and year for 195 countries and territories from 1990 to 2015. We analysed 38 risk-outcome pairs to generate estimates of smoking-attributable mortality and disease burden, as measured by disability-adjusted life-years (DALYs). We then performed a cohort analysis of smoking prevalence by birth-year cohort to better understand temporal age patterns in smoking. We also did a decomposition analysis, in which we parsed out changes in all-cause smoking-attributable DALYs due to changes in population growth, population ageing, smoking prevalence, and risk-deleted DALY rates. Finally, we explored results by level of development using the Socio-demographic Index (SDI). Worldwide, the age-standardised prevalence of daily smoking was 25·0% (95% uncertainty interval [UI] 24·2-25·7) for men and 5·4% (5·1-5·7) for women, representing 28·4% (25·8-31·1) and 34·4% (29·4-38·6) reductions, respectively, since 1990. A greater percentage of countries and territories achieved significant annualised rates of decline in smoking prevalence from 1990 to 2005 than in between 2005 and 2015; however, only four countries had significant annualised increases in smoking prevalence between 2005 and 2015 (Congo [Brazzaville] and Azerbaijan for men and Kuwait and Timor-Leste for women). In 2015, 11·5% of global deaths (6·4 million [95% UI 5·7-7·0 million]) were attributable to smoking worldwide, of which 52·2% took place in four countries (China, India, the USA, and Russia). Smoking was ranked among the five leading risk factors by DALYs in 109 countries and territories in 2015, rising from 88 geographies in 1990. In terms of birth cohorts, male smoking prevalence followed similar age patterns across levels of SDI, whereas much more heterogeneity was found in age patterns for female smokers by level of development. While smoking prevalence and risk-deleted DALY rates mostly decreased by sex and SDI quintile, population growth, population ageing, or a combination of both, drove rises in overall smoking-attributable DALYs in low-SDI to middle-SDI geographies between 2005 and 2015. The pace of progress in reducing smoking prevalence has been heterogeneous across geographies, development status, and sex, and as highlighted by more recent trends, maintaining past rates of decline should not be taken for granted, especially in women and in low-SDI to middle-SDI countries. Beyond the effect of the tobacco industry and societal mores, a crucial challenge facing tobacco control initiatives is that demographic forces are poised to heighten smoking's global toll, unless progress in preventing initiation and promoting cessation can be substantially accelerated. Greater success in tobacco control is possible but requires effective, comprehensive, and adequately implemented and enforced policies, which might in turn require global and national levels of political commitment beyond what has been achieved during the past 25 years. Bill & Melinda Gates Foundation and Bloomberg Philanthropies.", "Improving survival and extending the longevity of life for all populations requires timely, robust evidence on local mortality levels and trends. The Global Burden of Disease 2015 Study (GBD 2015) provides a comprehensive assessment of all-cause and cause-specific mortality for 249 causes in 195 countries and territories from 1980 to 2015. These results informed an in-depth investigation of observed and expected mortality patterns based on sociodemographic measures. We estimated all-cause mortality by age, sex, geography, and year using an improved analytical approach originally developed for GBD 2013 and GBD 2010. Improvements included refinements to the estimation of child and adult mortality and corresponding uncertainty, parameter selection for under-5 mortality synthesis by spatiotemporal Gaussian process regression, and sibling history data processing. We also expanded the database of vital registration, survey, and census data to 14 294 geography-year datapoints. For GBD 2015, eight causes, including Ebola virus disease, were added to the previous GBD cause list for mortality. We used six modelling approaches to assess cause-specific mortality, with the Cause of Death Ensemble Model (CODEm) generating estimates for most causes. We used a series of novel analyses to systematically quantify the drivers of trends in mortality across geographies. First, we assessed observed and expected levels and trends of cause-specific mortality as they relate to the Socio-demographic Index (SDI), a summary indicator derived from measures of income per capita, educational attainment, and fertility. Second, we examined factors affecting total mortality patterns through a series of counterfactual scenarios, testing the magnitude by which population growth, population age structures, and epidemiological changes contributed to shifts in mortality. Finally, we attributed changes in life expectancy to changes in cause of death. We documented each step of the GBD 2015 estimation processes, as well as data sources, in accordance with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER). Globally, life expectancy from birth increased from 61·7 years (95% uncertainty interval 61·4-61·9) in 1980 to 71·8 years (71·5-72·2) in 2015. Several countries in sub-Saharan Africa had very large gains in life expectancy from 2005 to 2015, rebounding from an era of exceedingly high loss of life due to HIV/AIDS. At the same time, many geographies saw life expectancy stagnate or decline, particularly for men and in countries with rising mortality from war or interpersonal violence. From 2005 to 2015, male life expectancy in Syria dropped by 11·3 years (3·7-17·4), to 62·6 years (56·5-70·2). Total deaths increased by 4·1% (2·6-5·6) from 2005 to 2015, rising to 55·8 million (54·9 million to 56·6 million) in 2015, but age-standardised death rates fell by 17·0% (15·8-18·1) during this time, underscoring changes in population growth and shifts in global age structures. The result was similar for non-communicable diseases (NCDs), with total deaths from these causes increasing by 14·1% (12·6-16·0) to 39·8 million (39·2 million to 40·5 million) in 2015, whereas age-standardised rates decreased by 13·1% (11·9-14·3). Globally, this mortality pattern emerged for several NCDs, including several types of cancer, ischaemic heart disease, cirrhosis, and Alzheimer's disease and other dementias. By contrast, both total deaths and age-standardised death rates due to communicable, maternal, neonatal, and nutritional conditions significantly declined from 2005 to 2015, gains largely attributable to decreases in mortality rates due to HIV/AIDS (42·1%, 39·1-44·6), malaria (43·1%, 34·7-51·8), neonatal preterm birth complications (29·8%, 24·8-34·9), and maternal disorders (29·1%, 19·3-37·1). Progress was slower for several causes, such as lower respiratory infections and nutritional deficiencies, whereas deaths increased for others, including dengue and drug use disorders. Age-standardised death rates due to injuries significantly declined from 2005 to 2015, yet interpersonal violence and war claimed increasingly more lives in some regions, particularly in the Middle East. In 2015, rotaviral enteritis (rotavirus) was the leading cause of under-5 deaths due to diarrhoea (146 000 deaths, 118 000-183 000) and pneumococcal pneumonia was the leading cause of under-5 deaths due to lower respiratory infections (393 000 deaths, 228 000-532 000), although pathogen-specific mortality varied by region. Globally, the effects of population growth, ageing, and changes in age-standardised death rates substantially differed by cause. Our analyses on the expected associations between cause-specific mortality and SDI show the regular shifts in cause of death composition and population age structure with rising SDI. Country patterns of premature mortality (measured as years of life lost [YLLs]) and how they differ from the level expected on the basis of SDI alone revealed distinct but highly heterogeneous patterns by region and country or territory. Ischaemic heart disease, stroke, and diabetes were among the leading causes of YLLs in most regions, but in many cases, intraregional results sharply diverged for ratios of observed and expected YLLs based on SDI. Communicable, maternal, neonatal, and nutritional diseases caused the most YLLs throughout sub-Saharan Africa, with observed YLLs far exceeding expected YLLs for countries in which malaria or HIV/AIDS remained the leading causes of early death. At the global scale, age-specific mortality has steadily improved over the past 35 years; this pattern of general progress continued in the past decade. Progress has been faster in most countries than expected on the basis of development measured by the SDI. Against this background of progress, some countries have seen falls in life expectancy, and age-standardised death rates for some causes are increasing. Despite progress in reducing age-standardised death rates, population growth and ageing mean that the number of deaths from most non-communicable causes are increasing in most countries, putting increased demands on health systems. Bill & Melinda Gates Foundation.", "The time has come for the world to acknowledge the unacceptability of the damage being done by the tobacco industry and work towards a world essentially free from the sale (legal and illegal) of tobacco products. A tobacco-free world by 2040, where less than 5% of the world's adult population use tobacco, is socially desirable, technically feasible, and could become politically practical. Three possible ways forward exist: so-called business-as-usual, with most countries steadily implementing the WHO Framework Convention on Tobacco Control (FCTC) provisions; accelerated implementation of the FCTC by all countries; and a so-called turbo-charged approach that complements FCTC actions with strengthened UN leadership, full engagement of all sectors, and increased investment in tobacco control. Only the turbo-charged approach will achieve a tobacco-free world by 2040 where tobacco is out of sight, out of mind, and out of fashion--yet not prohibited. The first and most urgent priority is the inclusion of an ambitious tobacco target in the post-2015 sustainable development health goal. The second priority is accelerated implementation of the FCTC policies in all countries, with full engagement from all sectors including the private sector--from workplaces to pharmacies--and with increased national and global investment. The third priority is an amendment of the FCTC to include an ambitious global tobacco reduction goal. The fourth priority is a UN high-level meeting on tobacco use to galvanise global action towards the 2040 tobacco-free world goal on the basis of new strategies, new resources, and new players. Decisive and strategic action on this bold vision will prevent hundreds of millions of unnecessary deaths during the remainder of this century and safeguard future generations from the ravages of tobacco use." ]
what is saxitoxin	Harmful algae blooms have expanded greatly in recent decades, and their secreted toxins pose a severe threat to human health and marine ecosystems. Saxitoxin (STX) is a main paralytic shellfish poison naturally produced by marine microalgae of the genus	[ "Palytoxin (PTX) is a potent marine toxin that was originally found in soft corals from tropical areas of the Pacific Ocean. Soon after, its occurrence was observed in numerous other marine organisms from the same ecological region. More recently, several analogs of PTX were discovered, remarkably all from species of the dinoflagellate genus Ostreopsis. Since these dinoflagellates are also found in other tropical and even in temperate regions, the formerly unsuspected broad distribution of these toxins was revealed. Toxicological studies with these compounds shows repeatedly low LD50 values in different mammals, revealing an acute toxic effect on several organs, as demonstrated by different routes of exposure. Bioassays tested for some marine invertebrates and evidences from environmental populations exposed to the toxins also give indications of the high impact that these compounds may have on natural food webs. The recognition of its wide distribution coupled with the poisoning effects that these toxins can have on animals and especially on humans have concerned the scientific community. In this paper, we review the current knowledge on the effects of PTX and its analogs on different organisms, exposing the impact that these toxins may have in coastal ecosystems.", "Silver nanoparticles (AgNPs) are the most commercialized nanomaterial worldwide, mainly due to their microbicidal activity. Although, AgNPs have been shown to be toxic to aquatic species, their effect on endemic fish, like Goodeidae, has not been demonstrated. Endemic species are under strong pressures by anthropogenic contamination and destruction of their habitat; therefore, we studied adult Chapalichthys pardalis, an endemic fish of Mexico. We evaluated the toxic effect of AgNPs through oxidative stress, macromolecular and metabolic biomarkers. We determined the LC50 (96h) and performed subchronic tests (21days) using sublethal AgNPs concentrations (equivalent to CL1 and CL10). At the end of the bioassay, we quantified 10 stress biomarkers in the liver, gills, and muscle, including the antioxidant enzymes (superoxide dismutase [SOD], catalase [CAT], and glutathione [GPx]), thiobarbituric acid reactive species (TBARS), protein oxidation (CO), macromolecules (proteins, lipids, and carbohydrates), and metabolites (glucose and lactate). In addition, we determined the integrated biomarkers response (IBR). LC50 was of 10.32mgL-1. Results of subchronic exposure (21days) revealed that AgNPs produce oxidative stress in C. pardalis adults, as evidenced by a diminution in antioxidant enzymes activity and an increase in TBARS and oxidized proteins. AgNPs also diminished levels of macromolecules and generated a high-energy consumption, reflected in the reduction of glucose levels, although lactate levels were not altered. The IBR analysis evidenced that the largest effect was produced in organisms exposed to LC10, being the liver and gills the organs with the greatest damage. Results demonstrated that exposure to AgNPs induces acute and chronic toxic effects on C. pardalis and forewarns about the impact that these nanomaterials can exert on these ecologically relevant aquatic organisms.", "Palytoxin and its derivatives have been implicated in toxic events in humans following ingestion or inhalation, and many studies on the toxicities of these substances to animals, via various routes of administration, have been described. In this report, the toxicity of palytoxin to animals has been reviewed, with comments on possible mechanisms of action. Information required for the risk assessment of palytoxin and its derivatives is by no means complete, and recommendations for further studies, which may better inform regulatory decisions regarding these substances, are also discussed.", "Palytoxin isolated from the genus Palythoa is the most potent marine toxin known. The aim of the present study was to quantify palytoxin-induced cellular injury in the human intestinal cell line Caco-2. Cellular damage was measured by evaluating cell proliferation, cell membrane permeability, cell morphology and apoptotic markers. Furthermore, changes in F-actin were studied after exposure of cells to increasing amounts of palytoxin. The results show that cell proliferation decreased in a concentration-dependent manner with a mean IC(50) value of about 0.1 nM. A noticeable increase of cell detachment correlated with cell rounding and F-actin depolymerization was observed in palytoxin-treated cells. Moreover LDH was released from the cells in a dose and time dependent manner, although under these conditions there was no propidium iodide uptake. On the other hand, palytoxin impaired mitochondrial activity but other apoptotic markers, such as DNA fragmentation or caspases activation, were not observed. The results obtained in this paper suggest that the effects of palytoxin in Caco-2 cells were very potent and unspecific, since a primary necrosis and a secondary apoptosis seem to occur under these conditions.", "Harmful algal blooms of Alexandrium spp. dinoflagellates regularly occur in French coastal waters contaminating shellfish. Studies have demonstrated that toxic Alexandrium spp. disrupt behavioural and physiological processes in marine filter-feeders, but molecular modifications triggered by phycotoxins are less well understood. This study analyzed the mRNA levels of 7 genes encoding antioxidant/detoxifying enzymes in gills of Pacific oysters (Crassostrea gigas) exposed to a cultured, toxic strain of A. minutum, a producer of paralytic shellfish toxins (PST) or fed Tisochrysis lutea (T. lutea, formerly Isochrysis sp., clone Tahitian (T. iso)), a non-toxic control diet, in four repeated experiments. Transcript levels of sigma-class glutathione S-transferase (GST), glutathione reductase (GR) and ferritin (Fer) were significantly higher in oysters exposed to A. minutum compared to oysters fed T. lutea. The detoxification pathway based upon glutathione (GSH)-conjugation of toxic compounds (phase II) is likely activated, and catalyzed by GST. This system appeared to be activated in gills probably for the detoxification of PST and/or extra-cellular compounds, produced by A. minutum. GST, GR and Fer can also contribute to antioxidant functions to prevent cellular damage from increased reactive oxygen species (ROS) originating either from A. minutum cells directly, from oyster hemocytes during immune response, or from other gill cells as by-products of detoxification.", "In January 2003, the US Environmental Protection Agency sponsored a \"roundtable discussion\" to develop a consensus on the relationship between eutrophication and harmful algal blooms (HABs), specifically targeting those relationships for which management actions may be appropriate. Academic, federal, and state agency representatives were in attendance. The following seven statements were unanimously adopted by attendees based on review and analysis of current as well as pertinent previous data: 1) Degraded water quality from increased nutrient pollution promotes the development and persistence of many HABs and is one of the reasons for their expansion in the U.S. and the world; 2) The composition - not just the total quantity - of the nutrient pool impacts HABs; 3) High biomass blooms must have exogenous nutrients to be sustained; 4) Both chronic and episodic nutrient delivery promote HAB development; 5) Recently developed tools and techniques are already improving the detection of some HABs, and emerging technologies are rapidly advancing toward operational status for the prediction of HABs and their toxins; 6) Experimental studies are critical to further the understanding of the role of nutrients in HAB expression, and will strengthen prediction and mitigation of HABs; and 7) Management of nutrient inputs to the watershed can lead to significant reduction in HABs. Supporting evidence and pertinent examples for each consensus statement is provided herein.", "Microcystins (MCs) are a major group of potent cyanobacterial toxins found in freshwater and even brackish waterbodies. To understand the putative correlation between bioconcentration of MCs and antioxidant responses of the digestive gland of bivalves, Pacific oyster Crassostrea gigas and blue mussel Mytilus edulis were exposed to different concentrations (0.1, 1, 10 and 20μgL-1) of MC-Leucine-Arginine (LR) for seven days. MC-LR bioconcentrated in the digestive glands of both bivalves during exposure period. The levels were slightly reduced when the bivalves were exposed to seawater during depuration (7days), while approximately 0.1μgL-1 of MC-LR was observed in the 10 and 20μgL-1 exposed bivalves at the end of depuration. Intracellular malondialdehyde (MDA) and glutathione (GSH) levels were significantly elevated in the 10 and 20μgL-1 exposed bivalves at 7day, and the levels were maintained during depuration in both bivalves. Overall, significant higher levels of enzymatic activities of antioxidant defense systems such as glutathione S-transferase (GST), catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx) and glutathione reductase (GR) were observed in the 10 and 20μgL-1 exposed bivalves. Interestingly, most of higher levels of Pacific oyster were detected at exposure period, while blue mussel showed higher levels at depuration phase, suggesting a species-specific sensitivity upon MC-LR. These patterns were correlated with the bioconcentration patterns of MC-LR as Pacific oyster was highly accumulated by MC-LR during exposure period, but blue mussel showed prolonged high levels of MC-LR for depuration phase. Our results will be useful to understand species-specific bioconcentration of MC-LR in bivalves and their effects on intracellular oxidative status via accumulation.", "The FETAX (frog embryo teratogenesis assay Xenopus) is considered a useful bioassay to detect health hazard substances. In the study of the marine toxin palytoxin (PTX), FETAX has revealed evident impacts on embryo mortality, teratogenesis and growth at the two highest (370 and 37nM) concentrations used. Significant mortality rates, peaks in the number of malformed embryos and delays in growth were found, while the total sample number fell by about 80% at the end of the assay with the concentrated dose. The histological analysis to evaluate the morpho-functional induced modifications demonstrated damage to the nervous and muscle tissue, a general reduction in the size of the main inner visceral organs and severe injury to the heart structure in some specimens. No inflammatory response was observed.", "Saxitoxin (STX) is a neurotoxin produced by dinoflagellates in diverse species, such as Alexandrium spp., and it causes paralytic shellfish poisoning (PSP) in humans after the ingestion of contaminated shellfish. Recent studies have suggested that the immune functions of bivalves could be affected by harmful algae and/or by their toxins. Herein, hemocytes are the main effector cells of the immune cellular response. In this study, we evaluated the response of hemocytes from the mussel Mytilus chilensis to STX exposure in a primary culture. Cell cultures were characterized according to size and complexity, while reactive oxygen species (ROS) production was evaluated using a dichlorofluorescein diacetate (DCFH-DA) assay. Finally, phagocytic activity was measured using both flow cytometry and fluorescence microscopy assays. Additionally, gene transcription of candidate genes was evaluated by qPCR assays. The results evidenced that exposures to different concentrations of STX (1-100 nM) for 24 h did not affect cell viability, as determined by an MTT assay. However, when hemocytes were exposed for 4 or 16 h to STX (1-100 nM), there was a modulation of phagocytic activity and ROS production. Moreover, hemocytes exposed to 100 nM of STX for 4 or 16 h showed a significant increase in transcript levels of genes encoding for antioxidant enzymes (SOD, CAT), mitochondrial enzymes (COI, COIII, CYTB, ATP6, ND1) and ion channels (K+, Ca2+). Meanwhile, C-type lectin and toll-like receptor genes revealed a bi-phase transcriptional response after 16 and 24-48 h of exposure to STX. These results suggest that STX can negatively affect the immunocompetence of M. chilensis hemocytes, which were capable of responding to STX exposure in vitro by increasing the mRNA levels of antioxidant enzymes.", "Ocean acidification processes are major threats to marine calcifying organisms, mostly affecting biomineralization related processes. Abiotic stressors acting on marine systems do not act alone, rather in a combination of multiple stressors, especially in coastal habitats such as estuaries, where anthropogenic and environmental pressures are high. Arsenic (As) is a widely distributed contaminant worldwide and its toxicity has been studied on a variety of organisms. However, the effect of low pH on the toxicity of As on marine organisms is unknown. Here, we studied the combined effects of ocean acidification and As exposure on two closely related oyster species (Crassostrea angulata and Crassostrea gigas), by use of a biochemical approach. Oxidative stress related parameters were studied along with the assessment of biomineralization enzymes activity after 28days of exposure. Results showed that both species were sensitive to all tested conditions (low pH, As and pH+As), showing enhancement of antioxidant and biotransformation defenses and impairment of biomineralization processes. Glutathione S-transferases (GSTs) activity were significantly higher in oysters exposed to As, showing activation of detoxification mechanisms, and a lower GSTs activity was observed in low pH+As condition, indicating an impact on the oysters capacity to detoxify As in a low pH scenario. Carbonic anhydrase (CA) activity was significantly lower in all tested conditions, showing to be affected by both As and low pH, whereas the combined effect of low pH+As was not different from the effect of low pH alone. Multivariate analysis of biochemical data allowed for the comparison of both species performance, showing a clear distinction of response in both species. C. gigas presented overall higher enzymatic activity (GSTs; superoxide dismutase; catalase; CA and acid phosphatase) and higher cytosolic GSH content in As exposed oysters than C. angulata. Results obtained indicate a higher tolerance capacity of the Pacific oyster C. gigas towards the tested conditions." ]
miRNA199a-based post-transcriptional detargeting for hepatocellular carcinoma gene therapy	A gene therapeutic platform needs to be both efficient and safe. The criterion of safety is particularly important for diseases like hepatocellular carcinoma (HCC), which develop in a background of an already compromised liver. Gene vectors can be constructed either by targeting HCC or by detargeting liver and/or other major organs. miRNA-based negative detargeting has gained considerable attention in recent times due to its effectiveness and the ease with which it can be adapted into current gene delivery vectors. In this study, we provide a proof-of-concept using miRNA199a as a negative targeting agent. We introduced vectors harboring reporters with miRNA199a binding sites in cells expressing high endogenous levels of miRNA199a and compared the reporter expression in HCC cells with low endogenous miRNA199a. We observed that the expression of reporters with miRNA199a binding sites is significantly inhibited in miRNA199a-positive cells, whereas minimal effect was observed in miRNA199a-negative HCC cells. In addition, we created a post-transcriptionally regulated suicide gene therapeutic system based on cytosine deaminase (CD)/5-fluorocytosine (5-FC) exploiting miRNA199a binding sites and observed significantly lower cell death for miRNA199a-positive cells. Furthermore, we observed a decrease in the levels of miRNA199 in 3D tumorspheres of miRNA199a-positive Hepa1-6 cells and a reduction in the inhibition of reporter expression after transfection in these 3D models when compared with 2D Hepa1-6 cells. In summary, we provide evidence of miRNA199a-based post-transcriptional detargeting with relevance to HCC gene therapy.	[ "Targeted gene delivery relies on the ability to limit the expression of a transgene within a defined cell/tissue population. MicroRNAs represent a class of highly powerful and effective regulators of gene expression that act by binding to a specific sequence present in the corresponding messenger RNA. Involved in almost every aspect of cellular function, many miRNAs have been discovered with expression patterns specific to developmental stage, lineage, cell-type, or disease stage. Exploiting the binding sites of these miRNAs allows for construction of targeted gene delivery platforms with a diverse range of applications. Here, we summarize studies that have utilized miRNA-regulated systems to achieve targeted gene delivery for both research and therapeutic purposes. Additionally, we identify criteria that are important for the effectiveness of a particular miRNA for such applications and we also discuss factors that have to be taken into consideration when designing miRNA-regulated expression cassettes.", "In this study, we explored the actions of miR-199a/b-5p during hepatocellular carcinoma (HCC) progression and its potential target genes. Through heatmap miRNA expression analysis of 15 matched HCC tumor and adjacent non-tumor liver tissues from the TCGA database, we detected 19 mRNAs that were upregulated and 13 that were downregulated specifically in HCC. Among these, miR-199 family members were downregulated in HCC tumors and cell lines, as compared to controls. Low miR-199a/b-5p expression was also associated with poor overall survival of HCC patients. miR-199a/b-5p overexpression in HCC cell lines inhibited cell proliferation, migration and invasion, both in vitro and in vivo. In addition, miR199-a/b-5p post-transcriptionally suppressed Rho-associated coiled-coil kinase 1 (ROCK1). This in turn led to inhibition of ROCK1/MLC and PI3K/Akt signaling, which is necessary for HCC proliferation and metastasis. These results indicate that miR-199a/b acts as tumor suppressors in HCC and represent promising therapeutic targets.", "Golgi protein 73 (GP73) as a potential serum marker for hepatocellular carcinoma (HCC) has not been validated in large cohort studies. Furthermore, its significance in the assessment of tumour recurrence after HCC resection remains unknown. The aim of this study was to determine the value of serum GP73 in the diagnosis of HCC. Serum GP73 and alpha-fetoprotein (AFP) were compared in a total of 4217 human subjects in this multicentre study, including 1690 healthy adults, 337 hepatitis B virus (HBV) carriers, 512 patients with cirrhosis, 789 patients with HCC, 61 patients with other malignant liver lesions, 206 patients with benign liver lesions and 622 patients with 14 different kinds of non-liver cancers. The main outcome measures were the specificity and sensitivity of GP73 in patients at risk for the development of HCC. Using 8.5 relative units as a cut-off value, the sensitivity and specificity of serum GP73 for HCC were 74.6% (95% CI 71.5% to 77.6%) and 97.4% (95% CI 96.8 to 98.3%), compared with 58.2% (95% CI 55.2% to 62.1%) and 85.3% (95% CI 83.4% to 88.1%) for AFP (p<0.001) using 35 ng/ml as a cut-off value. The GP73 level was significantly increased in patients with HCC compared with healthy controls (14.7 vs 1.2, p<0.001). Although GP73 levels in HBV carriers (2.9) and patients with cirrhosis (4.7) were somewhat elevated, they were much lower than that in patients with HCC (p<0.001). GP73 decreased following surgical resection of HCC lesions and increased with tumour recurrence. Fourteen types of non-liver cancers were analysed; all the benign and other malignant liver lesions had moderate elevations of GP73, albeit at a much lower level than in HCC. GP73 is an accurate serum marker for the detection of HCC and its recurrence after surgery, with higher sensitivity and specificity than AFP. Clinical implementation of serum GP73 measurement as a standard test for HCC is recommended.", "We have shown previously that transgene expression can be suppressed in hematopoietic cells using vectors that are responsive to microRNA (miRNA) regulation. Here we investigate the potential of this approach for more sophisticated control of transgene expression. Analysis of the relationship between miRNA expression levels and target mRNA suppression suggested that suppression depends on a threshold miRNA concentration. Using this information, we generated vectors that rapidly adjust transgene expression in response to changes in miRNA expression. These vectors sharply segregated transgene expression between closely related states of therapeutically relevant cells, including dendritic cells, hematopoietic and embryonic stem cells, and their progeny, allowing positive/negative selection according to the cells' differentiation state. Moreover, two miRNA target sites were combined to restrict transgene expression to a specific cell type in the liver. Notably, the vectors did not detectably perturb endogenous miRNA expression or regulation of natural targets. The properties of miRNA-regulated vectors should allow for safer and more effective therapeutic applications.", "TNF-related apoptosis-inducing ligand (TRAIL) functions as a soluble cytokine and has been demonstrated significant antitumor activity against a variety of cancer cell lines without toxicity to most normal cells. Cisplatin is a potent anticancer agent and is widely used in the clinical for treatment of human cancers. Adeno-associated virus (AAV2) is a promising gene delivery vehicle for its advantage of low pathogenicity and long-term gene expression. However, lack of tissue specificity caused low efficiency of AAV transfer to target cells. The promoter of human telomerase reverse transcriptase (hTERT) is a good candidate to enhance targeting efficiency of AAV in cancer cells. Although AAV-mediated TRAIL controlled by hTERT promoter (AAV-hTERT-TRAIL) has obvious antitumor activity, the tumor cannot be completely eradicated. In this study, we first examined the effectiveness of combination therapy of cisplatin and AAV-hTERT-TRAIL on human hepatocellular carcinoma (HCC) in vitro and in vivo. For in vitro experiments, tumor cell lines were treated with cisplatin, virus, or both. The transgene TRAIL expression controlled by hTERT promoter was evaluated in BEL7404 HCC cell line. Cytotoxicity was performed by MTT analysis. Cell apoptosis was detected by flow cytometry analysis. The in vivo antitumor efficacy of combination treatment with cisplatin and AAV-hTERT-TRAIL was assessed in human hepatocellular carcinoma xenografts mouse model. The enhanced TRAIL expression was observed in BEL7404 cells treated with AAV-hTERT-TRAIL plus cisplatin. Treatment with both AAV-hTERT-TRAIL and cisplatin exhibited stronger cytotoxicity and induced more significant apoptosis in cancer cells compared with AAV-hTERT-TRAIL or cisplatin alone, respectively. Moreover, in animal experiments, the combined treatment greatly suppressed tumor growth and resulted in tumor cell death. AAV-mediated therapeutic gene expression in combination with chemotherapy provides a promising therapeutic strategy for human cancers. These data suggest that combined use of AAV-hTERT-TRAIL and cisplatin may have potential clinical application.", "Telomerase activity is a wide tumor marker. Human telomerase reverse transcriptase (hTERT), the catalytic subunit of the telomerase, is transcriptionally upregulated exclusively in about 90% of cancer cells. In this study, we constructed a novel adeno-associated virus (AAV) vector containing the human interferon-beta (hIFN-beta) gene under the control of hTERT promoter (AAV-hTERT-hIFN-beta) and investigated its antitumor effect against various human cancer cells in vitro. AAV-hTERT-hIFN-beta displayed cancer-specific hIFN-beta expression and cytotoxicity. The cytotoxic ratio was positively correlated with the time length of infection. AAV-hTERT-hIFN-beta-mediated apoptotic morphology was observed by transmission electron microscopy. Flow cytometry assay also revealed that the cytotoxicity of AAV-hTERT-hIFN-beta was mainly an apoptotic process. These data indicate that AAV in combination with hTERT-mediated therapeutic gene expression may open new possibilities for long-lasting and targeting gene therapy of varieties of cancers.", "Thyroid cancer incidence is rapidly increasing. Papillary Thyroid Carcinoma (PTC), the most frequent hystotype, usually displays good prognosis, but no effective therapeutic options are available for the fraction of progressive PTC patients. BRAF and RET/PTC are the most frequent driving genetic lesions identified in PTC. We developed two complementary in vitro models based on RET/PTC1 oncogene, starting from the hypothesis that miRNAs modulated by a driving PTC-oncogene are likely to have a role in thyroid neoplastic processes. Through this strategy, we identified a panel of deregulated miRNAs. Among these we focused on miR-199a-3p and showed its under-expression in PTC specimens and cell lines. We demonstrated that miR-199a-3p restoration in PTC cells reduces MET and mTOR protein levels, impairs migration and proliferation and, more interesting, induces lethality through an unusual form of cell death similar to methuosis, caused by macropinocytosis dysregulation. Silencing MET or mTOR, both involved in survival pathways, does not recapitulate miR-199a-3p-induced cell lethality, thus suggesting that the cooperative regulation of multiple gene targets is necessary. Integrated analysis of miR-199a-3p targets unveils interesting networks including HGF and macropinocytosis pathways. Overall our results indicate miR-199a-3p as a tumor suppressor miRNA in PTC." ]
Searching for Patterns in Protein Sequences	All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for "repetition", an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust "familiarity" definition between arbitrary sets of sequences.	[ "Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB-disp, should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields.", "Many cell signaling events are coordinated by intrinsically disordered protein regions (IDRs) that undergo multisite Serine/Threonine phosphorylation. The conformational properties of these IDRs prior to and following multisite phosphorylation are directly relevant to understanding their functions. Here, we present results from biophysical studies and molecular simulations that quantify the conformational properties of an 81-residue IDR from the S. cerevisiae transcription factor Ash1. We show that the unphosphorylated Ash1 IDR adopts coil-like conformations that are expanded and well-solvated. This result contradicts inferences regarding global compaction that are derived from heuristics based on amino acid compositions for IDRs with low proline contents. Upon phosphorylation at ten distinct sites, the global conformational properties of pAsh1 are indistinguishable from those of unphosphorylated Ash1. This insensitivity derives from compensatory changes to the pattern of local and long-range intrachain contacts. We show that the conformational properties of Ash1 and pAsh1 can be explained in terms of the linear sequence patterning of proline and charged residues vis-à-vis all other residues. The sequence features of the Ash1 IDR are shared by many other IDRs that undergo multisite phosphorylation. Accordingly, we propose that our findings might be generalizable to other IDRs involved in cell signaling.", "The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.edu/charmm_ff.shtml), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins.", "The isolated N-terminal Src homology 3 (SH3) domain of Drosophila drk exists in equilibrium between folded and unfolded states in aqueous buffer near neutral pH. Nuclear magnetic resonance spectra recorded on both states simultaneously exhibit an approximate 1:1 ratio of protein conformations. The folded form is similar to other known SH3 structures, especially the N-terminal SH3 domain of the mammalian homologue GRB2. A stretch of sequential amide-amide nuclear Overhauser effect cross-peaks for resonances of the unfolded state is observed in a region corresponding to beta-strands in the folded state. The results suggest that turn-like conformations may be preferentially sampled in the folding pathway for this predominantly beta-structured SH3 domain. In addition, a stable turn at Leu-28 is observed in the unfolded but not in the folded state. Comparison of this unfolded form with a denatured state in 2 M guanidine hydrochloride shows that, while both are highly disordered, these states are not identical and more residual structure is present under nondenaturing conditions." ]
Genetic architecture studies of complex traits and diseases in Africa	Human genetic studies have long been vastly Eurocentric, raising a key question about the generalizability of these study findings to other populations. Because humans originated in Africa, these populations retain more genetic diversity, and yet individuals of African descent have been tremendously underrepresented in genetic studies. The diversity in Africa affords ample opportunities to improve fine-mapping resolution for associated loci, discover novel genetic associations with phenotypes, build more generalizable genetic risk prediction models, and better understand the genetic architecture of complex traits and diseases subject to varying environmental pressures. Thus, it is both ethically and scientifically imperative that geneticists globally surmount challenges that have limited progress in African genetic studies to date. Additionally, African investigators need to be meaningfully included, as greater inclusivity and enhanced research capacity afford enormous opportunities to accelerate genomic discoveries that translate more effectively to all populations. We review the advantages, challenges, and examples of genetic architecture studies of complex traits and diseases in Africa. For example, with greater genetic diversity comes greater ancestral heterogeneity; this higher level of understudied diversity can yield novel genetic findings, but some methods that assume homogeneous population structure and work well in European populations may work less well in the presence of greater heterogeneity in African populations. Consequently, we advocate for methodological development that will accelerate studies important for all populations, especially those currently underrepresented in genetics.	[ "Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped on the Illumina 610-Quad arrays and 112 Mexicans genotyped on Affymetrix 500K platform. Intersecting these data with previously collected high-density SNP data from 4,305 individuals, we use principal component analysis and clustering methods FRAPPE and STRUCTURE to investigate genome-wide patterns of African, European, and Native American population structure within and among Hispanic/Latino populations. Comparing autosomal, X and Y chromosome, and mtDNA variation, we find evidence of a significant sex bias in admixture proportions consistent with disproportionate contribution of European male and Native American female ancestry to present-day populations. We also find that patterns of linkage-disequilibria in admixed Hispanic/Latino populations are largely affected by the admixture dynamics of the populations, with faster decay of LD in populations of higher African ancestry. Finally, using the locus-specific ancestry inference method LAMP, we reconstruct fine-scale chromosomal patterns of admixture. We document moderate power to differentiate among potential subcontinental source populations within the Native American, European, and African segments of the admixed Hispanic/Latino genomes. Our results suggest future genome-wide association scans in Hispanic/Latino populations may require correction for local genomic ancestry at a subcontinental scale when associating differences in the genome with disease risk, progression, and drug efficacy, as well as for admixture mapping.", "Human genetic diversity is shaped by both demographic and biological factors and has fundamental implications for understanding the genetic basis of diseases. We studied 938 unrelated individuals from 51 populations of the Human Genome Diversity Panel at 650,000 common single-nucleotide polymorphism loci. Individual ancestry and population substructure were detectable with very high resolution. The relationship between haplotype heterozygosity and geography was consistent with the hypothesis of a serial founder effect with a single origin in sub-Saharan Africa. In addition, we observed a pattern of ancestral allele frequency distributions that reflects variation in population dynamics among geographic regions. This data set allows the most comprehensive characterization to date of human genetic variation.", "For many decades, access to human biological samples, such as cells, tissues, organs, blood, and sub-cellular materials such as DNA, for use in biomedical research, has been central in understanding the nature and transmission of diseases across the globe. However, the limitations of current ethical and regulatory frameworks in sub-Saharan Africa to govern the collection, export, storage and reuse of these samples have resulted in inconsistencies in practice and a number of ethical concerns for sample donors, researchers and research ethics committees. This paper examines stakeholders' perspectives of and responses to the ethical issues arising from these research practices. We employed a qualitative strategy of inquiry for this research including in-depth interviews and focus group discussions with key research stakeholders in Kenya (Nairobi and Kilifi), and Ghana (Accra and Navrongo). The stakeholders interviewed emphasised the compelling scientific importance of sample export, storage and reuse, and acknowledged the existence of some structures governing these research practices, but they also highlighted the pressing need for a number of practical ethical concerns to be addressed in order to ensure high standards of practice and to maintain public confidence in international research collaborations. These concerns relate to obtaining culturally appropriate consent for sample export and reuse, understanding cultural sensitivities around the use of blood samples, facilitating a degree of local control of samples and sustainable scientific capacity building. Drawing on these findings and existing literature, we argue that the ethical issues arising in practice need to be understood in the context of the interactions between host research institutions and local communities and between collaborating institutions. We propose a set of 'key points-to-consider' for research institutions, ethics committees and funding agencies to address these issues.", "Large whole-genome sequencing projects have provided access to much rare variation in human populations, which is highly informative about population structure and recent demography. Here, we show how the age of rare variants can be estimated from patterns of haplotype sharing and how these ages can be related to historical relationships between populations. We investigate the distribution of the age of variants occurring exactly twice (ƒ(2) variants) in a worldwide sample sequenced by the 1000 Genomes Project, revealing enormous variation across populations. The median age of haplotypes carrying ƒ(2) variants is 50 to 160 generations across populations within Europe or Asia, and 170 to 320 generations within Africa. Haplotypes shared between continents are much older with median ages for haplotypes shared between Europe and Asia ranging from 320 to 670 generations. The distribution of the ages of ƒ(2) haplotypes is informative about their demography, revealing recent bottlenecks, ancient splits, and more modern connections between populations. We see the effect of selection in the observation that functional variants are significantly younger than nonfunctional variants of the same frequency. This approach is relatively insensitive to mutation rate and complements other nonparametric methods for demographic inference.", "Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.", "The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The multiple sequentially Markovian coalescent (MSMC) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 years ago, including the bottleneck in the peopling of the Americas and separations within Africa, East Asia and Europe." ]
Molecular Targets for Metastatic Castration Resistant Prostate Cancer	Prostate cancer (PCa) is one of the most common malignancies in men and is a major contributor to cancer related deaths worldwide. Metastatic spread and disease progression under androgen deprivation therapy signify the onset of metastatic castration resistant prostate cancer (mCRPCa)-the lethal form of the disease, which severely deteriorates the quality of life of patients. Over the last decade, tremendous progress has been made toward identifying appropriate molecular targets that could enable efficient	[ "Prostate cancer (PCa) is the most common malignancy in men worldwide, leading to substantial morbidity and mortality. At present, imaging of PCa has become increasingly important for staging, restaging, and treatment selection. Until recently, choline-based positron emission tomography/computed tomography (PET/CT) represented the state-of-the-art radionuclide imaging technique for these purposes. However, its application is limited to patients with high PSA levels and Gleason scores. Prostate-specific membrane antigen (PSMA) is a promising new target for specific imaging of PCa, because it is upregulated in the majority of PCa. Moreover, PSMA can serve as a target for therapeutic applications. Currently, several small-molecule PSMA ligands with excellent in vivo tumor targeting characteristics are being investigated for their potential in theranostic applications in PCa. Here, a review of the recent developments in PSMA-based diagnostic imaging and therapy in patients with PCa with radiolabeled PSMA ligands is provided.", "(177)Lu-617-prostate-specific membrane antigen (PSMA) ligand seems to be a promising tracer for radionuclide therapy of progressive prostate cancer. However, there are no published data regarding the radiation dose given to the normal tissues. The aim of the present study was to estimate the pretreatment radiation doses in patients who will undergo radiometabolic therapy using a tracer amount of (177)Lu-labeled PSMA ligand. The study included seven patients with progressive prostate cancer with a mean age of 63.9 ± 3.9 years. All patients had prior PSMA positron emission tomography (PET) imaging and had intense tracer uptake at the lesions. The injected (177)Lu-PSMA-617 activity ranged from 185 to 210 MBq with a mean of 192.6 ± 11.0 MBq. To evaluate bone marrow absorbed dose 2-cc blood samples were withdrawn in short variable times (3, 15, 30, 60, and 180 min and 24, 48, and 120 h) after injection. Whole-body images were obtained at 4, 24, 48, and 120 h post-injection (p.i.). The geometric mean of anterior and posterior counts was determined through region of interest (ROI) analysis. Attenuation correction was applied using PSMA PET/CT images. The OLINDA/EXM dosimetry program was used for curve fitting, residence time calculation, and absorbed dose calculations. The calculated radiation-absorbed doses for each organ showed substantial variation. The highest radiation estimated doses were calculated for parotid glands and kidneys. Calculated radiation-absorbed doses per megabecquerel were 1.17 ± 0.31 mGy for parotid glands and 0.88 ± 0.40 mGy for kidneys. The radiation dose given to the bone marrow was significantly lower than those of kidney and parotid glands (p < 0.05). The calculated radiation dose to bone marrow was 0.03 ± 0.01 mGy/MBq. Our first results suggested that (177)Lu-PSMA-617 therapy seems to be a safe method. The dose-limiting organ seems to be the parotid glands rather than kidneys and bone marrow. The lesion radiation doses are within acceptable ranges; however, there is a substantial individual variance so patient dosimetry seems to be mandatory.", "Prostate cancer is the most common cancer diagnosis made in men with more than 160 000 new cases each year in the United States. Although it often has an indolent course, prostate cancer remains the third-leading cause of cancer death in men. When prostate cancer is suspected, tissue biopsy remains the standard of care for diagnosis. However, the identification and characterization of the disease have become increasingly precise through improved risk stratification and advances in magnetic resonance and functional imaging, as well as from the emergence of biomarkers. Multiple management options now exist for men diagnosed with prostate cancer. Active surveillance (the serial monitoring for disease progression with the intent to cure) appears to be safe and has become the preferred approach for men with less-aggressive prostate cancer, particularly those with a prostate-specific antigen level of less than 10 ng/mL and Gleason score 3 + 3 tumors. Surgery and radiation continue to be curative treatments for localized disease but have adverse effects such as urinary symptoms and sexual dysfunction that can negatively affect quality of life. For metastatic disease, chemotherapy as initial treatment now appears to extend survival compared with androgen deprivation therapy alone. New vaccines, hormonal therapeutics, and bone-targeting agents have demonstrated efficacy in men with metastatic prostate cancer resistant to traditional hormonal therapy. Advances in the diagnosis and treatment of prostate cancer have improved the ability to stratify patients by risk and allowed clinicians to recommend therapy based on cancer prognosis and patient preference. Initial treatment with chemotherapy can improve survival compared with androgen deprivation therapy. Abiraterone, enzalutamide, and other agents can improve outcomes in men with metastatic prostate cancer resistant to traditional hormonal therapy.", "The aim of this evaluation was to identify the first indicators of efficacy for 225Ac-labeled prostate-specific membrane antigen (PSMA)-617 therapy in a retrospectively analyzed group of patients. Methods: Forty patients with metastatic castration-resistant prostate cancer were selected for treatment with three 100 kBq/kg cycles of 225Ac-PSMA-617 at 2-mo intervals. Prostate-specific antigen (PSA) and blood cell count were measured every 4 wk. PSMA PET/CT or PSMA SPECT/CT were used for baseline staging and imaging follow-up at month 6. Follow-up included the duration of PSA response and radiologic progression-free survival at month 6. Patient histories were reviewed for the duration of previous treatment lines, and a swimmer plot was used to intraindividually compare the duration of tumor control by PSMA therapy versus prior treatment modalities. Results: Thirty-one of 40 patients were treated per protocol. Five patients discontinued treatment because of nonresponse, and 4 because of xerostomia. Of the 38 patients surviving at least 8 wk, 24 (63%) had a PSA decline of more than 50%, and 33 (87%) had a PSA response of any degree. The median duration of tumor control under 225Ac-PSMA-617 last-line therapy was 9.0 mo; 5 patients had an enduring response of more than 2 y. Because all patients had advanced disease, this result compares favorably with the tumor control rates associated with earlier-phase disease; the most common preceding first-, second-, third-, and fourth-line therapies were abiraterone (median duration 10.0 mo), docetaxel (6.5 mo), enzalutamide (6.5 mo), and cabazitaxel (6.0 mo), respectively. Conclusion: A positive response for surrogate parameters demonstrates remarkable antitumor activity for 225Ac-PSMA-617. Swimmer-plot analysis indicates a promising duration of tumor control, especially considering the unfavorable prognostic profile of the selected advanced-stage patients. Xerostomia was the main reason patients discontinued therapy or refused additional administrations and was in the same dimension as nonresponse; this finding indicates that further modifications of the treatment regimen with regard to side effects might be necessary to further enhance the therapeutic range.", "The development of radiopharmaceuticals containing 225Ac for targeted alpha therapy is an active area of academic and commercial research worldwide. Despite promising results from recent clinical trials, 225Ac-radiopharmaceutical development still faces significant challenges that must be overcome to realize the widespread clinical use of 225Ac. Some of these challenges include the limited availability of the isotope, the challenging chemistry required to isolate 225Ac from any co-produced isotopes, and the need for stable targeting systems with high radiolabeling yields. Here we provide a review of available literature pertaining to these challenges in the 225Acradiopharmaceutical field and also provide insight into how performed and planned efforts at TRIUMF - Canada's particle accelerator centre - aim to address these issues.", "Actinium-225 and 213Bi have been used successfully in targeted alpha therapy (TAT) in preclinical and clinical research. This paper is a continuation of research activities aiming to expand the availability of 225Ac. The high-energy proton spallation reaction on natural thorium metal targets has been utilized to produce millicurie quantities of 225Ac. The results of sixteen irradiation experiments of thorium metal at beam energies between 78 and 192MeV are summarized in this work. Irradiations have been conducted at Brookhaven National Laboratory (BNL) and Los Alamos National Laboratory (LANL), while target dissolution and processing was carried out at Oak Ridge National Laboratory (ORNL). Excitation functions for actinium and thorium isotopes, as well as for some of the fission products, are presented. The cross sections for production of 225Ac range from 3.6 to 16.7mb in the incident proton energy range of 78-192MeV. Based on these data, production of curie quantities of 225Ac is possible by irradiating a 5.0gcm-2 232Th target for 10 days in either BNL or LANL proton irradiation facilities.", "(68)Ga-labeled, low-molecular-weight imaging agents that target the prostate-specific membrane antigen (PSMA) are increasingly used clinically to detect prostate and other cancers with positron emission tomography (PET). The goal of this study was to compare the pharmacokinetics of three PSMA-targeted radiotracers: (68)Ga-1, using DOTA-monoamide as the chelating agent; (68)Ga-2, containing the macrocyclic chelating agent p-SCN-Bn-NOTA; and (68)Ga-DKFZ-PSMA-11, currently in clinical trials, which uses the acyclic chelating agent, HBED-CC. The PSMA-targeting scaffold for all three agents utilized a similar Glu-urea-Lys-linker construct. Each radiotracer enabled visualization of PSMA+ PC3 PIP tumor, kidney, and urinary bladder as early as 15 min post-injection using small animal PET/computed tomography (PET/CT). (68)Ga-2 demonstrated the fastest rate of clearance from all tissues in this series and displayed higher uptake in PSMA+ PC3 PIP tumor compared to (68)Ga-1 at 1 h post-injection. There was no significant difference in PSMA+ PC3 PIP tumor uptake for the three agents at 2 and 3 h post-injection. (68)Ga-DKFZ-PSMA-11 demonstrated the highest uptake and retention in normal tissues, including kidney, blood, spleen, and salivary glands and PSMA-negative PC3 flu tumors up to 3 h post-injection. In this preclinical evaluation (68)Ga-2 had the most advantageous characteristics for PSMA-targeted PET imaging." ]
Polyethylene glycol-conjugated asparaginase (PEG-L- CHOP) in non-Hodgkin lymphoma in adult Chinese patients	The combination of chemotherapy and L-asparaginase (L-ASP) treatment significantly increased survival rate in an adult patient with extranodal natural killer (NK)/T-cell lymphoma (NKTCL). However, hypersensitivity reactions of L-ASP in some patients limited its application. Polyethylene glycol-conjugated asparaginase (PEG-ASP) has a lower immunogenicity and longer circulating half-life than unconjugated L-ASP, and has been reported to be effective and well-tolerated in children with acute lymphoblastic leukemia. Cyclophosphamide, hydroxydaunorubicin (doxorubicin), oncovin (vincristine), and prednisolone (CHOP) is the most common chemotherapy for non-Hodgkin lymphoma. In this report, we sought to study the efficacy and safety of PEG-L- CHOP in NKTCL in adult Chinese patients.	[ "Extranodal NK/T-Cell lymphoma, nasal type (NKTLN) is a disease that mainly affects the nasal cavity and the paranasal sinuses. Early nasal symptoms are nonspecific, simulating sinus infection. With disease progression, necrosis of the nasal mucosa increases, hindering histological diagnosis. Thus, multiple biopsies may be necessary until definitive diagnosis. Most studies on NKTLN address the hematological and immunological aspects of the disease. To present data from a Brazilian quaternary hospital, with emphasis on the clinical aspects of the disease, and to correlate the findings with the most recent literature data. Case study of seven patient files. Patients were evaluated on their medical history, number of biopsies necessary, association with Epstein-Barr virus, treatment, and outcome. All patients had nonspecific nasal complaints and underwent at least three cycles of antibiotic therapy. The earlier a biopsy was performed, the fewer biopsies were required to diagnose the disease and start treatment. However, this fact did not translate into better prognosis. The otolaryngologist plays a fundamental role in the prognosis of NKTLN and can shorten time between symptom onset and treatment of the patient.", "Epstein-Barr virus (EBV) is a lymphotropic herpesvirus. However, access to B lymphocytes during primary infection may be facilitated by replication in mucosal epithelial cells. Attachment and penetration of EBV into these two cell types are fundamentally different. Both the distribution of receptors and the cellular origin of the virus impact the efficiency of infection. Epithelial cells potentially offer a wide range of receptors with which virus can interact. We report here on analyses of epithelial cells expressing different combinations of receptors. We find that the stoichiometry of the virus glycoprotein complex that includes gHgL and gp42 affects the use of gHgL not just for entry into epithelial cells but also for attachment. Penetration can be mediated efficiently with either a coreceptor for gp42 or gHgL, but the use of gHgL for attachment as well as penetration greatly compromises its ability to mediate entry.", "In contrast to that in children, pharmacokinetic, pharmacodynamic, and safety information on pegaspargase in adults is very limited. We administered a single intravenous dose of pegaspargase (2000 IU/m2) as part of a standard frontline induction regimen to 25 adults with newly diagnosed acute lymphoblastic leukemia (ALL), and obtained serum samples on several time points. The population mean peak serum concentration of asparaginase enzymatic activity was 1 IU/mL, the elimination half-life was 7 days, and the volume of distribution was 2.43 L/m2. After the single dose, asparagine deamination was complete in all patients after 2 hours, and in 100%, 81%, and 44% on days 14, 21, and 28, respectively. A pharmocodynamic correlation model showed minimal enzymatic activity of 0.2 IU/mL for optimal asparagine depletion. The kinetic posthoc analyses demonstrated enzymatic activity for 3 weeks or more. One patient developed neutralizing antiasparaginase antibodies on day 22 after administration. Pegaspargase was well tolerated, with few grade 3/4 side effects. No allergic reactions or pancreatitis were observed. In adults aged 55 years or younger, pegaspargase produces a long duration of asparagine depletion and can be given intravenously, with a safety profile that is similar to equivalent multiple doses of intramuscular Escherichia coli asparaginase.", "The major Epstein-Barr virus (EBV) envelope glycoprotein, gp350, was purified from the B95-8 cell line and analyzed for its ability to mediate virus attachment to the isolated EBV/C3d receptor (CR2) of human B lymphocytes. Purified gp350 and EBV, but not cytomegalovirus, exhibited dose-dependent binding to purified CR2 in dot blot immunoassays. Binding was inhibited by certain monoclonal antibodies to CR2 and to gp350. Liposomes bearing incorporated gp350 bound to CR2-positive B-cell lines but not to CR2-negative lines. Liposome binding was also inhibited by the OKB7 anti-CR2 monoclonal antibody. A computer-generated comparison of the deduced gp350 amino acid sequence with that of the human C3d complement fragment revealed two regions of significant primary sequence homology, a finding which suggests that a common region on these two unrelated proteins may be involved in CR2 binding." ]
Mylohyoid kinematics influence the selection of the most probable motor chain	The ability to understand intentions based on another's movements is crucial for human interaction. This ability has been ascribed to the so-called motor chaining mechanism: anytime a motor chain is activated (e.g., grasp-to-drink), the observer attributes to the agent the corresponding intention (i.e., to drink) from the first motor act (i.e., the grasp). However, the mechanisms by which a specific chain is selected in the observer remain poorly understood. In the current study, we investigate the possibility that in the absence of discriminative contextual cues, slight kinematic variations in the observed grasp inform mapping to the most probable chain. Chaining of motor acts predicts that, in a sequential grasping task (e.g., grasp-to-drink), electromyographic (EMG) components that are required for the final act [e.g., the mouth-opening mylohyoid (MH) muscle] show anticipatory activation. To test this prediction, we used MH EMG, transcranial magnetic stimulation (TMS; MH motor-evoked potentials), and predictive models of movement kinematics to measure the level and timing of MH activation during the execution (Experiment 1) and the observation (Experiment 2) of reach-to-grasp actions. We found that MH-related corticobulbar excitability during grasping observation varied as a function of the goal (to drink or to pour) and the kinematics of the observed grasp. These results show that subtle changes in movement kinematics drive the selection of the most probable motor chain, allowing the observer to link an observed act to the agent's intention.	[ "Amidst controversy about methodology and safety, intraoperative neurophysiology has entered a new era of increasingly routine transcranial and direct electrical brain stimulation for motor evoked potential (MEP) monitoring. Based on literature review and illustrative clinical experience, this tutorial aims to present a balanced overview for experienced practitioners, surgeons and anesthesiologists as well as those new to the field. It details the physiologic basis, indications and methodology of current MEP monitoring techniques, evaluates their safety, explores interpretive controversies and outlines some applications and results, including aortic aneurysm, intramedullary spinal cord tumor, spinal deformity, posterior fossa tumor, intracranial aneurysm and peri-rolandic brain surgeries. The many advances in motor system assessment achieved in the last two decades undoubtedly improve monitoring efficacy without unduly compromising safety. Future studies and experience will likely clarify existing controversies and bring further advances.", "The inferior part of the parietal lobe (IPL) is known to play a very important role in sensorimotor integration. Neurons in this region code goal-related motor acts performed with the mouth, with the hand and with the arm. It has been demonstrated that most IPL motor neurons coding a specific motor act (e.g., grasping) show markedly different activation patterns according to the final goal of the action sequence in which the act is embedded (grasping for eating or grasping for placing). Some of these neurons (parietal mirror neurons) show a similar selectivity also during the observation of the same action sequences when executed by others. Thus, it appears that the neuronal response occurring during the execution and the observation of a specific grasping act codes not only the executed motor act, but also the agent's final goal (intention).In this work we present a biologically inspired neural network architecture that models mechanisms of motor sequences execution and recognition. In this network, pools composed of motor and mirror neurons that encode motor acts of a sequence are arranged in form of action goal-specific neuronal chains. The execution and the recognition of actions is achieved through the propagation of activity bursts along specific chains modulated by visual and somatosensory inputs.The implemented spiking neuron network is able to reproduce the results found in neurophysiological recordings of parietal neurons during task performance and provides a biologically plausible implementation of the action selection and recognition process.Finally, the present paper proposes a mechanism for the formation of new neural chains by linking together in a sequential manner neurons that represent subsequent motor acts, thus producing goal-directed sequences.", "This work aimed to study mylohyoid motor-evoked potentials (MHMEPs) and examined if it is related to chronic stroke dysphagia. Conduction time (CT) and amplitudes of the right and left MHMEPs in response to focal cortical magnetic stimulations over affected and unaffected hemispheres were recorded in 16 stroke patients with aspiration (n = 9) or residue (n = 7) and compared with eight control patients. In control group, MHMEPs were present on ipsilateral and contralateral sides after stimulation of both hemispheres and permitted to determine a dominant hemisphere. In stroke patients, after stimulation of the affected hemisphere, ipsilateral MEPs had a longer CT and lower amplitudes in patients with aspiration compared with patients with residue or control patients (P < 0.05). Contralateral CT was not different between the three groups, but amplitudes were lower in patients with residue and aspiration than in control patients (P < 0.01). In the unaffected hemisphere, MHMEPs were present, and not different between the three groups for the ipsilateral side and amplitudes were decreased in contralateral side in patients with residue. In conclusion, MHMEP alterations of the affected hemisphere related to chronic stroke dysphagia severity and were closed to normal in the unaffected hemisphere.", "To compare the effects of isoflurane and propofol on intraoperative neurophysiological monitoring (IONM) during spinal surgery. Thirty-five patients were randomly assigned to receive isoflurane (n = 17) or propofol (n = 18) anesthesia. Somatosensory evoked potentials (SEPs) following posterior tibial nerve stimulation were recorded before induction as baselines. Isoflurane concentrations and propofol infusions were adjusted to obtain four pre-determined BIS ranges: 65-55, 55-45, 45-35 and 35-25. For each range, a stable state was maintained for at least 10 min to perform IONM. The SEP latency P40 and amplitude P40-N50, the onset latency and amplitude of transcranial motor evoked potentials (tcMEPs), and threshold intensity of triggered electromyographic activity (EMG) following pedicle screw stimulation were statistically analyzed. Compared with baseline values, P40 latency increased and P40-N50 amplitude decreased after anesthesia with isoflurane or propofol. Isoflurane caused a dose-dependent depression of SEPs, but propofol did not. TcMEPs were recordable and stable in all patients receiving propofol in each BIS range, but only recordable in 10 (58.8%) receiving isoflurane with BIS >55, and 3 (17.8%) with BIS <55. No difference was noted in triggered EMG. Isoflurane inhibited IONM more than propofol. Propofol is recommended for critical spinal surgery, particularly when motor pathway function is monitored.", "Induction of a seizure in a normal subject with trains of repetitive transcranial magnetic stimulation (rTMS) applied in close succession suggested that short inter-train intervals, a parameter not considered in our previous safety studies, may not be safe. Here, we evaluate the safety of different inter-train intervals for rTMS in 10 healthy volunteers. Ten rTMS trains at 20 Hz for 1.6 s and a stimulus intensity of 110% of motor threshold (MT) were found to be safe at the inter-train interval of 5 s. However, inter-train intervals of 1 s or less were unsafe for trains of 20 Hz for 1.6 s and stimulus intensities higher than 100% of MT. Based on these results, we propose safety guidelines for inter-train intervals at different stimulus intensities. We also analyzed the stimulus parameters, used in 3 studies, that led to seizures in normal subjects. One seizure was due to short inter-train intervals, one was likely related to intense individual rTMS trains close to the limit of our previous safety recommendations, and one was likely due to a combination of these two factors. To provide an additional safety margin, we suggest reducing the duration for individual rTMS trains by 25% from our previous recommendations. Updated safety tables currently in use at our institution are provided.", "The authors conducted a study to evaluate repetitive transcranial electrical stimulation (TES) to assess spinal cord motor tract function in individuals undergoing spine surgery, with emphasis on safety and efficacy. Somatosensory evoked potentials (SSEPs) were elicited using standard technique. Muscle electromyographic values were measured in response to a three- or four-pulse train of stimulation delivered to the motor cortex via subdermal electrodes. They also evaluated whether changes in the minimum stimulus intensity (that is, threshold level) needed to elicit a response from a given muscle predict motor status immediately postoperatively, as well as whether changes in SSEP response amplitude and latency predict sensory status immediately postoperatively. Anesthesia was routinely induced with intravenous propofol and remifentanil, supplemented with inhaled nitrous oxide. Use of neuromuscular block was avoided after intubation. Satisfactory monitoring of muscle response to threshold-level repetitive TES was achieved in all but nine of the 194 patients studied. In contrast, cortical SSEP responses could not be elicited in 42 of 194 individuals. In cases in which responses were present, TES-based evoked responses proved to be extremely accurate for predicting postoperative motor status. Somatosensory evoked potential monitoring was nearly as accurate for predicting postoperative sensory status. There were frequent instances of postoperative motor or sensory deficit that were not predicted by SSEP- and TES-based monitoring, respectively. There were no adverse events attributable to TES-based monitoring, although since this study ended we have had a single adverse event attributable to threshold-level repetitive TES. Intraoperative threshold-level repetitive TES-based monitoring of central motor conduction has proven to be a simple, safe, and highly accurate technique for the prevention or minimization of inadvertent motor deficit during surgery involving the spine or spinal cord.", "To determine whether, and under which conditions, transcranial electrical stimulation (TES) and transcranial magnetic stimulation (TMS) can activate similar neuronal structures of the human motor cortex, as indicated by electromyographic recordings. Focal TMS was performed on three subjects inducing a postero-anterior directed current (p-a), TES with postero-anteriorly (p-a) and latero-medially (l-m) oriented electrodes. We analyzed the onset latencies and amplitudes (single-pulse) and intracortical inhibition and excitation (paired-pulse). TMS p-a and TES p-a produced muscle responses with the same onset latency, while TES l-m led to 1.4-1.9 ms shorter latencies. Paired-pulse TMS p-a and TES p-a induced inhibition at short inter-stimulus intervals (ISI) (maximum: 2-3 ms) and facilitation at longer ISIs (maximum: 10 ms). No inhibition but a strong facilitation was obtained from paired-pulse TES l-m (ISIs 1-5 ms). Our findings support the hypothesis, that current direction is the most relevant factor in determining the mode of activation for both TMS and TES: TMS p-a and TES p-a are likely to activate the corticospinal neurons indirectly. In contrast, TES l-m may preferentially activate the corticospinal fibres directly, distant of the neuronal body. TES is a suitable tool to induce intracortical inhibition and excitation." ]
Herpesviruses assemble and escape from host cells	Many viruses, enveloped or non-enveloped, remodel host membrane structures for their replication, assembly and escape from host cells. Herpesviruses are important human pathogens and cause many diseases. As large enveloped DNA viruses, herpesviruses undergo several complex steps to complete their life cycles and produce infectious progenies. Firstly, herpesvirus assembly initiates in the nucleus, producing nucleocapsids that are too large to cross through the nuclear pores. Nascent nucleocapsids instead bud at the inner nuclear membrane to form primary enveloped virions in the perinuclear space followed by fusion of the primary envelopes with the outer nuclear membrane, to translocate the nucleocapsids into the cytoplasm. Secondly, nucleocapsids obtain a series of tegument proteins in the cytoplasm and bud into vesicles derived from host organelles to acquire viral envelopes. The vesicles are then transported to and fuse with the plasma membrane to release the mature virions to the extracellular space. Therefore, at least two budding and fusion events take place at cellular membrane structures during herpesviruses assembly and egress, which induce membrane deformations. In this review, we describe and discuss how herpesviruses exploit and remodel host membrane structures to assemble and escape from the host cell.	[ "Adenovirus (Ad) infection is concluded by assembly of virions in the cell nucleus followed by lysis of cells by an unknown mechanism. We have described an Ad nuclear membrane glycoprotein of 11,600 kDa (E3-11.6K) which is encoded by the E3 transcription unit and which is synthesized in small amounts from the E3 promoter at early stages of infection but in large amounts from the major late promoter at very late stages of infection. We now report that E3-11.6K is required for the efficient lysis (death) of Ad-infected cells, and we propose that the function of E3-11.6K is to mediate the release of Ad progeny from infected cells. We have renamed E3-11.6K the Ad death protein (ADP). Virus mutants that lack ADP replicated as well as adp+ Ad, but the cells lysed more slowly, virus release from the cell was retarded, and the plaques were small and developed slowly. Cells infected with adp+ viruses began to lyse at 2 or 3 days postinfection (p.i.) and were completely lysed by 5 or 6 days p.i. In contrast, cells infected with adp mutants did not begin significant lysis until 5 or 6 days p.i. Cell lysis and viability were determined by plaque size, extracellular virus, cell morphology, release of lactate dehydrogenase, trypan blue exclusion, the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay for mitochondrial activity, RNA degradation, and DNA degradation as determined by agarose gel electrophoresis and the terminal deoxynucleotidyltransferase end labeling assay. Protein synthesis was almost nonexistent at 3 days p.i. in cells infected with adp+ Ads, but it was still increasing in cells infected with adp mutants. Host cell protein synthesis was undetectable at 1 day p.i. in cells infected with adp+ Ads or adp mutants. Cells infected with adp mutants showed Ad cytopathic effect at 1 or 2 days p.i. in that they rounded up and detached, but the cells remained metabolically active and intact for >5 days p.i. When examined by electron microscopy, the nuclei were extremely swollen and full of virus, and the nuclear membrane appeared to be intact. ADP is unrelated in sequence to other known cell death-promoting proteins.", "Viruses are intracellular parasites that use the host cell they infect to produce new infectious progeny. Distinct steps of the virus life cycle occur in association with the cytoskeleton or cytoplasmic membranes, which are often modified during infection. Plus-stranded RNA viruses induce membrane proliferations that support the replication of their genomes. Similarly, cytoplasmic replication of some DNA viruses occurs in association with modified cellular membranes. We describe how viruses modify intracellular membranes, highlight similarities between the structures that are induced by viruses of different families and discuss how these structures could be formed.", "Herpes simplex virus type 1 (HSV-1) glycoprotein H (gH) is essential for virus entry into cells and forms a hetero-oligomer with a newly described viral glycoprotein, gL. Normal folding, posttranslational processing, and intracellular transport of both gH and gL depend upon the coexpression of gH and gL in cells infected with vaccinia virus vectors (L. Hutchinson, H. Browne, V. Wargent, N. Davis-Poynter, S. Primorac, K. Goldsmith, A. C. Minson, and D. C. Johnson, J. Virol. 66:2240-2250, 1992). Homologs of gH and gL have been found in herpesviruses of all subgroups, and thus it appears likely that the gH-gL complex serves a highly conserved function during herpesvirus penetration into cells. To examine the role of gL in the infectious cycle of HSV-1, a mutant HSV-1 unable to express gL was constructed by inserting a lacZ gene cassette into the coding sequences of the UL1 (gL) gene. Because gL was found to be essential for virus replication, cell lines capable of expressing gL were constructed to complement the virus mutant. In the absence of gL, virus particles were produced, and these particles reached the cell surface; however, gL-negative particles purified from infected cells were also deficient in gH. Mutant virions lacking gH and gL were able to adsorb onto cells but were unable to enter cells and initiate an infection. Further, the role of gL in fusion of infected cells was reexamined. A mutation in HSV-1 (804) which produces the syncytial phenotype had previously been mapped to a region of the HSV-1 genome which includes the UL1 gene and no other open reading frame. However, in contrast to this previous report, we found that the syncytial mutation in 804 affects the UL53 gene, which encodes gK, a gene commonly mutated in syncytial viruses.", "Herpesvirus capsids collect along the inner surface of the nuclear envelope and bud into the perinuclear space. Enveloped virions then fuse with the outer nuclear membrane (NM). We previously showed that herpes simplex virus (HSV) glycoproteins gB and gH act in a redundant fashion to promote fusion between the virion envelope and the outer NM. HSV mutants lacking both gB and gH accumulate enveloped virions in herniations, vesicles that bulge into the nucleoplasm. Earlier studies had shown that HSV mutants lacking the viral serine/threonine kinase US3 also accumulate herniations. Here, we demonstrate that HSV gB is phosphorylated in a US3-dependent manner in HSV-infected cells, especially in a crude nuclear fraction. Moreover, US3 directly phosphorylated the gB cytoplasmic (CT) domain in in vitro assays. Deletion of gB in the context of a US3-null virus did not add substantially to defects in nuclear egress. The majority of the US3-dependent phosphorylation of gB involved the CT domain and amino acid T887, a residue present in a motif similar to that recognized by US3 in other proteins. HSV recombinants lacking gH and expressing either gB substitution mutation T887A or a gB truncated at residue 886 displayed substantial defects in nuclear egress. We concluded that phosphorylation of the gB CT domain is important for gB-mediated fusion with the outer NM. This suggested a model in which the US3 kinase is incorporated into the tegument layer (between the capsid and envelope) in HSV virions present in the perinuclear space. By this packaging, US3 might be brought close to the gB CT tail, leading to phosphorylation and triggering fusion between the virion envelope and the outer NM.", "The late stages of assembly of herpes simplex virus (HSV) and other herpesviruses are not well understood. Acquisition of the final virion envelope apparently involves interactions between viral nucleocapsids coated with tegument proteins and the cytoplasmic domains of membrane glycoproteins. This promotes budding of virus particles into cytoplasmic vesicles derived from the trans-Golgi network or endosomes. The identities of viral membrane glycoproteins and tegument proteins involved in these processes are not well known. Here, we report that HSV mutants lacking two viral glycoproteins, gD and gE, accumulated large numbers of unenveloped nucleocapsids in the cytoplasm. These aggregated capsids were immersed in an electron-dense layer that appeared to be tegument. Few or no enveloped virions were observed. More subtle defects were observed with an HSV unable to express gD and gI. A triple mutant lacking gD, gE, and gI exhibited more severe defects in envelopment. We concluded that HSV gD and the gE/gI heterodimeric complex act in a redundant fashion to anchor the virion envelope onto tegument-coated capsids. In the absence of either one of these HSV glycoproteins, envelopment proceeds; however, without both gD and gE, or gE/gI, there is profound inhibition of cytoplasmic envelopment.", "Monospecific antisera to herpes simplex virus type 1 (HSV-1) glycoproteins gB, gC, and gD were used to identify the HSV-1-specific glycoproteins associated with the nuclear fraction as compared with those associated with cytoplasmic fraction, whole-cell lysates, and purified virions. The results indicate that a predominance of HSV glycoprotein precursors pgC(105), pgB(110), and pgD(52) is associated with the nuclear fraction. Treatment of the nuclear fraction with the enzyme endo-beta-N-acetylglucosaminidase H indicated that the lower-molecular-weight glycoproteins are sensitive to this endoglycosidase. These results suggest that in the nuclear fraction of HSV-1-infected cells virus-specific glycoproteins gB, gC, and gD are predominately in the high-mannose precursor form; however, detectable amounts of the fully glycosylated forms of gC and gD were also found.", "Lamins are intermediate filament proteins that form a network lining the inner nuclear membrane. They provide mechanical strength to the nuclear envelope, but also appear to have many other functions as reflected in the array of diseases caused by lamin mutations. Unlike other intermediate filament proteins, they do not self-assemble into 10 nm filaments in vitro and their in vivo organization is uncertain. We have recently re-examined the organization of a simple B-type lamina in Xenopus oocytes [Goldberg, Huttenlauch, Hutchison and Stick (2008) J. Cell Sci. 121, 215-225] and shown that it consists of tightly packed 8-10 nm filaments with regular cross-connections, tightly opposed to the membrane. When lamin A is expressed in oocytes, it forms organized bundles on top of the B lamina. This has led to a new model for lamina organization which is discussed in the present paper." ]
Sulfur-Based Composite Materials for Lithium-Sulfur Batteries	Lithium-sulfur batteries (LSBs) represent a promising energy storage technology, and they show potential for next-generation high-energy systems due to their high specific capacity, abundant constitutive resources, non-toxicity, low cost, and environment friendliness. Unlike their ubiquitous lithium-ion battery counterparts, the application of LSBs is challenged by several obstacles, including short cycling life, limited sulfur loading, and severe shuttling effect of polysulfides. To make LSBs a viable technology, it is very important to design and synthesize outstanding cathode materials with novel structures and properties. In this review, we summarize recent progress in designs, preparations, structures, and properties of cathode materials for LSBs, emphasizing binary, ternary, and quaternary sulfur-based composite materials. We especially highlight the utilization of carbons to construct sulfur-based composite materials in this exciting field. An extensive discussion of the emerging challenges and possible future research directions for cathode materials for LSBs is provided.	[ "Lithium-sulphur batteries have high theoretical energy density and potentially low cost, but significant challenges such as severe capacity degradation prevent its widespread adoption. Here we report a new design of lithium-sulphur battery using electrically connected graphite and lithium metal as a hybrid anode to control undesirable surface reactions on lithium. Lithiated graphite placed in front of the lithium metal functions as an artificial, self-regulated solid electrolyte interface layer to actively control the electrochemical reactions and minimize the deleterious side reactions, leading to significant performance improvements. Lithium-sulphur cells incorporating this hybrid anodes deliver capacities of >800 mAh g(-1) for 400 cycles at a high rate of 1,737 mA g(-1), with only 11% capacity fade and a Coulombic efficiency >99%. This simple hybrid concept may also provide scientific strategies for protecting metal anodes in other energy-storage devices.", "The loss of sulfur cathode material as a result of polysulfide dissolution causes significant capacity fading in rechargeable lithium/sulfur cells. Here, we use a chemical approach to immobilize sulfur and lithium polysulfides via the reactive functional groups on graphene oxide. This approach enabled us to obtain a uniform and thin (around tens of nanometers) sulfur coating on graphene oxide sheets by a simple chemical reaction-deposition strategy and a subsequent low-temperature thermal treatment process. Strong interaction between graphene oxide and sulfur or polysulfides enabled us to demonstrate lithium/sulfur cells with a high reversible capacity of 950-1400 mA h g(-1), and stable cycling for more than 50 deep cycles at 0.1C (1C = 1675 mA g(-1)).", "Sulfur has a high specific capacity of 1673 mAh/g as lithium battery cathodes, but its rapid capacity fading due to polysulfides dissolution presents a significant challenge for practical applications. Here we report a hollow carbon nanofiber-encapsulated sulfur cathode for effective trapping of polysulfides and demonstrate experimentally high specific capacity and excellent electrochemical cycling of the cells. The hollow carbon nanofiber arrays were fabricated using anodic aluminum oxide (AAO) templates, through thermal carbonization of polystyrene. The AAO template also facilitates sulfur infusion into the hollow fibers and prevents sulfur from coating onto the exterior carbon wall. The high aspect ratio of the carbon nanofibers provides an ideal structure for trapping polysulfides, and the thin carbon wall allows rapid transport of lithium ions. The small dimension of these nanofibers provides a large surface area per unit mass for Li(2)S deposition during cycling and reduces pulverization of electrode materials due to volumetric expansion. A high specific capacity of about 730 mAh/g was observed at C/5 rate after 150 cycles of charge/discharge. The introduction of LiNO(3) additive to the electrolyte was shown to improve the Coulombic efficiency to over 99% at C/5. The results show that the hollow carbon nanofiber-encapsulated sulfur structure could be a promising cathode design for rechargeable Li/S batteries with high specific energy.", "A hollow carbon nanofiber hybrid nanostructure anchored with titanium dioxide (HCNF@TiO2) was prepared as a matrix for effective trapping of sulfur and polysulfides as a cathode material for Li-S batteries. The synthesized composites were characterized and examined by X-ray diffraction, nitrogen adsorption-desorption measurements, field-emission scanning electron microscopy, scanning transmission electron microscopy, and electrochemical methods such as galvanostatic charge/discharge, rate performance, and electrochemical impedance spectroscopy tests. The obtained HCNF@TiO2-S composite showed a clear core-shell structure with TiO2 nanoparticles coating the surface of the HCNF and sulfur homogeneously distributed in the coating layer. The HCNF@TiO2-S composite exhibited much better electrochemical performance than the HCNF-S composite, which delivered an initial discharge capacity of 1040 mA h g(-1) and maintained 650 mAh g(-1) after 200 cycles at a 0.5 C rate. The improvements of electrochemical performances might be attributed to the unique hybrid nanostructure of HCNF@TiO2 and good dispersion of sulfur in the HCNF@TiO2-S composite.", "A space-confined \"sauna\" reaction system is introduced for the simultaneous reduction and functionalization of graphene oxide to unique graphene-sulfur hybrid nanosheets, in which thin layers of amorphous sulfur are tightly anchored on the graphene sheet via strong chemical bonding. Upon being used as the cathode material in lithium-sulfur batteries, the as-synthesized composite shows an excellent electrochemical performance.", "Microporous carbon polyhedrons (MCPs) are encapsulated into polyacrylonitrile (PAN) nanofibers by electrospinning the mixture of MCPs and PAN. Subsequently, the as-prepared MCPs-PAN nanofibers are employed as sulfur immobilizer for lithium-sulfur battery. Here, the S/MCPs-PAN multicomposites integrate the advantage of sulfur/microporous carbon and sulfurized PAN. Specifically, with large pore volume, MCPs inside PAN nanofibers provide a sufficient sulfur loading. While PAN-based nanofibers offer a conductive path and matrix. Therefore, the electrochemical performance is significantly improved for the S/MCPs-PAN multicomposite with a suitable sulfur content in carbonate-based electrolyte. At the current density of 160 mA g-1sulfur, the S/MPCPs-PAN composite delivers a large discharge capacity of 789.7 mAh g-1composite, high Coulombic efficiency of about 100% except in the first cycle, and good capacity retention after 200 cycles. In particular, even at 4 C rate, the S/MCPs-PAN composite can still release the discharge capacity of 370 mAh g-1composite. On the contrary, the formation of the thick SEI layer on the surface of nanofibers with a high sulfur content are observed, which is responsible for the quick capacity deterioration of the sulfur-based composite in carbonate-based electrolyte. This design of the S/MCPs-PAN multicomposite is helpful for the fabrication of stable Li-S battery.", "Lithium-sulfur batteries have attracted attention due to their six-fold specific energy compared with conventional lithium-ion batteries. Dissolution of lithium polysulfides, volume expansion of sulfur and uncontrollable deposition of lithium sulfide are three of the main challenges for this technology. State-of-the-art sulfur cathodes based on metal-oxide nanostructures can suppress the shuttle-effect and enable controlled lithium sulfide deposition. However, a clear mechanistic understanding and corresponding selection criteria for the oxides are still lacking. Herein, various nonconductive metal-oxide nanoparticle-decorated carbon flakes are synthesized via a facile biotemplating method. The cathodes based on magnesium oxide, cerium oxide and lanthanum oxide show enhanced cycling performance. Adsorption experiments and theoretical calculations reveal that polysulfide capture by the oxides is via monolayered chemisorption. Moreover, we show that better surface diffusion leads to higher deposition efficiency of sulfide species on electrodes. Hence, oxide selection is proposed to balance optimization between sulfide-adsorption and diffusion on the oxides.", "Phase-controlled nickel sulfide (Ni3 S4 and NiS1.03 ) nanoparticle (NP)/nitrogen-doped graphene (NG) composites are prepared through a facile one-pot hydrothermal process. The composites show ultrahigh capacity retentions of 98.87% and 95.94% for Ni3 S4 /NG and NiS1.03 /NG electrodes, respectively, as anode materials for lithium ion batteries.", "Nitrogen-doped carbon (NDC) spheres with abundant 22 nm mesopores and 0.5 nm micropores are obtained by directly carbonization of nitrogen-contained metal organic framework (MOF) nanocrystals. Large S8 and small S2-4 molecules are successfully infiltrated into 22 nm mesopores and 0.5 nm micropores, respectively. We successfully investigate the effect of sulfur immobilization in mesopores and micropores on the electrochemical performance of lithium-sulfur (Li-S) battery based on NDC-sulfur hybrid cathodes. The large S8 molecules in 22 nm mesopores can be removed by a prolonged heat treatment, with only small molecules of S2-4 immobilized in micropores of NDC matrices. The NDC/S2-4 hybrid exhibits excellent cycling performance, high Coulombic efficiency, and good rate capability as cathode for Li-S batteries. The confinement of smaller S2-4 molecules in the micropores of NDS efficiently avoids the loss of active sulfur and formation of soluble high-order Li polysulfides. The porous carbon can buffer the volume expansion and contraction changes, promising a stable structure for cathode. Furthermore, N doping in MOF-derived carbon not only facilitates the fast charge transfer but also is helpful in building a stronger interaction between carbon and sulfur, strengthening immobilization ability of S2-4 in micropores. The NDS-sulfur hybrid cathode exhibits a reversible capacity of 936.5 mAh g(-1) at 100th cycle with a Coulombic efficiency of 100% under a current density of 335 mA g(-1). It displays a superior rate capability performance, delivering a capacity of 632 mAh g(-1) at a high rate of 5 A g(-1). This uniquely porous NDC derived from MOF nanocrystals could be applied in related high-energy storage devices.", "Chemistry at the cathode/electrolyte interface plays an important role for lithium-sulfur batteries in which stable cycling of the sulfur cathode requires confinement of the lithium polysulfide intermediates and their fast electrochemical conversion on the electrode surface. While many materials have been found to be effective for confining polysulfides, the underlying chemical interactions remain poorly understood. We report a new and general lithium polysulfide-binding mechanism enabled by surface oxidation layers of transition-metal phosphide and chalcogenide materials. We for the first time find that CoP nanoparticles strongly adsorb polysulfides because their natural oxidation (forming Co-O-P-like species) activates the surface Co sites for binding polysulfides via strong Co-S bonding. With a surface oxidation layer capable of confining polysulfides and an inner core suitable for conducting electrons, the CoP nanoparticles are thus a desirable candidate for stabilizing and improving the performance of sulfur cathodes in lithium-sulfur batteries. We demonstrate that sulfur electrodes that hold a high mass loading of 7 mg cm-2 and a high areal capacity of 5.6 mAh cm-2 can be stably cycled for 200 cycles. We further reveal that this new surface oxidation-induced polysulfide-binding scheme applies to a series of transition-metal phosphide and chalcogenide materials and can explain their stabilizing effects for lithium-sulfur batteries." ]
Effects of Metabolic Syndrome, Obesity, and Gut Microbiome on Osteoarthritis	Metabolic syndrome is characterized by obesity, hyperglycemia, hypertension, insulin resistance, and dyslipidemia. Metabolic syndrome is associated with osteoarthritis (OA), but it is unclear if the association is attributable to increased mechanical loading on joints caused by obesity or other aspects of metabolic syndrome. Here we examined the effects of altered metabolism, obesity, and the gut microbiome on load-induced OA.	[ "To evaluate anterior cruciate ligament transection (ACLT) and destabilization of the medial meniscus (DMM) surgical instability models of osteoarthritis (OA) in the 129/SvEv mouse knee joint. Micro-surgical techniques were used to perform ACLT or DMM under direct visualization. Histological scoring was performed on multiple sections to assess cartilage damage across the entire joint. The ACLT model gave severe OA, chondrogenesis of the joint capsule and, in some cases, severe subchondral erosion of the posterior tibial plateau. Surgical DMM was less invasive than the ACLT procedure and resulted in lesions primarily on the central weight-bearing region of the medial tibial plateau and medial femoral condyles. Lesions in the DMM model progressed from mild-to-moderate OA at 4 weeks, to moderate-to-severe OA at 8 weeks post-surgery. Destruction of the subchondral bone was never observed in the DMM model. ACLT is not recommended in the mouse due to the high surgical proficiency required and the development of severe OA that may involve subchondral bone erosion. The severity and location of lesions following DMM are consistent with lesions observed in aged spontaneous mouse models of OA. The DMM model has sufficient sensitivity to show disease modification, as observed with the ADAMTS-5 knock out (KO) mouse. The DMM model should be a first choice to challenge mice with gene deletions of potential targets in OA.", "While it is widely accepted that obesity is associated with low-grade systemic inflammation, the molecular origin of the inflammation remains unknown. Here, we investigated the effect of endotoxin-induced inflammation via TLR4 signaling pathway at both systemic and intestinal levels in response to a high-fat diet. C57BL/6J and TLR4-deficient C57BL/10ScNJ mice were maintained on a low-fat (10 kcal % fat) diet (LFD) or a high-fat (60 kcal % fat) diet (HFD) for 8 weeks. HFD induced macrophage infiltration and inflammation in the adipose tissue, as well as an increase in the circulating proinflammatory cytokines. HFD increased both plasma and fecal endotoxin levels and resulted in dysregulation of the gut microbiota by increasing the Firmicutes to Bacteriodetes ratio. HFD induced the growth of Enterobecteriaceae and the production of endotoxin in vitro. Furthermore, HFD induced colonic inflammation, including the increased expression of proinflammatory cytokines, the induction of Toll-like receptor 4 (TLR4), iNOS, COX-2, and the activation of NF-κB in the colon. HFD reduced the expression of tight junction-associated proteins claudin-1 and occludin in the colon. HFD mice demonstrated higher levels of Akt and FOXO3 phosphorylation in the colon compared to the LFD mice. While the body weight of HFD-fed mice was significantly increased in both TLR4-deficient and wild type mice, the epididymal fat weight and plasma endotoxin level of HFD-fed TLR4-deficient mice were 69% and 18% of HFD-fed wild type mice, respectively. Furthermore, HFD did not increase the proinflammatory cytokine levels in TLR4-deficient mice. HFD induces inflammation by increasing endotoxin levels in the intestinal lumen as well as in the plasma by altering the gut microbiota composition and increasing its intestinal permeability through the induction of TLR4, thereby accelerating obesity.", "Obesity plays a causative role in the pathogenesis of the metabolic syndrome. Adipokines may link obesity to its co-morbidities. Most adipokines with pro-inflammatory properties are overproduced with increasing adiposity, while some adipokines with anti-inflammatory or insulin-sensitizing properties, like adiponectin are decreased. This dysregulation of adipokine production may promote obesity-linked metabolic disorders and cardiovascular disease. Besides considering adipokines, this review will also highlight the cellular key players and molecular mechanisms involved in adipose inflammation. Targeting the changes in the cellular composition of adipose tissue, the underlying molecular mechanisms, and the altered production of adipokines may have therapeutic potential in the management of the metabolic syndrome.", "New therapeutic targets for noncognitive reductions in energy intake, absorption, or storage are crucial given the worldwide epidemic of obesity. The gut microbial community (microbiota) is essential for processing dietary polysaccharides. We found that conventionalization of adult germ-free (GF) C57BL/6 mice with a normal microbiota harvested from the distal intestine (cecum) of conventionally raised animals produces a 60% increase in body fat content and insulin resistance within 14 days despite reduced food intake. Studies of GF and conventionalized mice revealed that the microbiota promotes absorption of monosaccharides from the gut lumen, with resulting induction of de novo hepatic lipogenesis. Fasting-induced adipocyte factor (Fiaf), a member of the angiopoietin-like family of proteins, is selectively suppressed in the intestinal epithelium of normal mice by conventionalization. Analysis of GF and conventionalized, normal and Fiaf knockout mice established that Fiaf is a circulating lipoprotein lipase inhibitor and that its suppression is essential for the microbiota-induced deposition of triglycerides in adipocytes. Studies of Rag1-/- animals indicate that these host responses do not require mature lymphocytes. Our findings suggest that the gut microbiota is an important environmental factor that affects energy harvest from the diet and energy storage in the host. Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AY 667702--AY 668946)." ]
Predictive Models of Housing Instability and Homelessness	To develop and test predictive models of housing instability and homelessness based on responses to a brief screening instrument administered throughout the Veterans Health Administration (VHA).	[ "Understanding how to identify the social determinants of health from electronic health records (EHRs) could provide important insights to understand health or disease outcomes. We developed a methodology to capture 2 rare and severe social determinants of health, homelessness and adverse childhood experiences (ACEs), from a large EHR repository. We first constructed lexicons to capture homelessness and ACE phenotypic profiles. We employed word2vec and lexical associations to mine homelessness-related words. Next, using relevance feedback, we refined the 2 profiles with iterative searches over 100 million notes from the Vanderbilt EHR. Seven assessors manually reviewed the top-ranked results of 2544 patient visits relevant for homelessness and 1000 patients relevant for ACE. word2vec yielded better performance (area under the precision-recall curve [AUPRC] of 0.94) than lexical associations (AUPRC = 0.83) for extracting homelessness-related words. A comparative study of searches for the 2 phenotypes revealed a higher performance achieved for homelessness (AUPRC = 0.95) than ACE (AUPRC = 0.79). A temporal analysis of the homeless population showed that the majority experienced chronic homelessness. Most ACE patients suffered sexual (70%) and/or physical (50.6%) abuse, with the top-ranked abuser keywords being \"father\" (21.8%) and \"mother\" (15.4%). Top prevalent associated conditions for homeless patients were lack of housing (62.8%) and tobacco use disorder (61.5%), while for ACE patients it was mental disorders (36.6%-47.6%). We provide an efficient solution for mining homelessness and ACE information from EHRs, which can facilitate large clinical and genetic studies of these social determinants of health.", "The study explored disparities in housing status among veterans with general medical, cognitive, and behavioral health conditions. Multinomial mixed-effects models estimated the relationship between medical, cognitive, and behavioral health comorbidities and housing instability among veterans enrolled in the Veterans Health Administration (VHA) (N=1,582,125) who responded to the Homelessness Screening Clinical Reminder for homelessness and risk during a three-month period. Veterans were two or more times as likely to screen positive for homelessness or risk if they had a diagnosis of a cognitive or behavioral health conditions in the study. Findings related to general medical conditions were inconsistent. The study found disparities in housing instability among VHA outpatients with cognitive and behavioral health conditions, suggesting the need to identify veterans with these conditions experiencing housing instability and the need to develop appropriate interventions to mitigate homelessness or risk.", "Traditionally, patient groups with a phenotype are selected through rule-based definitions whose creation and validation are time-consuming. Machine learning approaches to electronic phenotyping are limited by the paucity of labeled training datasets. We demonstrate the feasibility of utilizing semi-automatically labeled training sets to create phenotype models via machine learning, using a comprehensive representation of the patient medical record. We use a list of keywords specific to the phenotype of interest to generate noisy labeled training data. We train L1 penalized logistic regression models for a chronic and an acute disease and evaluate the performance of the models against a gold standard. Our models for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.90, 0.89, and 0.86, 0.89, respectively. Local implementations of the previously validated rule-based definitions for Type 2 diabetes mellitus and myocardial infarction achieve precision and accuracy of 0.96, 0.92 and 0.84, 0.87, respectively.We have demonstrated feasibility of learning phenotype models using imperfectly labeled data for a chronic and acute phenotype. Further research in feature engineering and in specification of the keyword list can improve the performance of the models and the scalability of the approach. Our method provides an alternative to manual labeling for creating training sets for statistical models of phenotypes. Such an approach can accelerate research with large observational healthcare datasets and may also be used to create local phenotype models.", "This study examined factors associated with lifetime experience of homelessness among young adults. Data were analyzed for 14,888 young adults (mean+/-SD age 21.97+/-1.77; 7,037 men and 7,851 women) who participated in the National Longitudinal Study of Adolescent Health (Add Health), a U.S. nationally representative, population-based sample. Data were collected from young adults through computer-assisted interviews six years after they had enrolled in the study as adolescents. Variables that have been associated with lifetime homelessness in at least one service sample were mapped to Add Health survey items. Data were analyzed by logistic regression. A total of 682 respondents (4.6%) were classified as ever being homeless. Several factors related to childhood experiences of poor family functioning, socioeconomic disadvantage, and separation from parents or caregivers were independently associated with ever being homeless. Other significant independent factors included current socioeconomic difficulty, mental health problems, and addiction problems. Indicators of involvement in crime and addiction problems with gambling and alcohol were not independently associated with homelessness. The findings underscore the relationship between specific indicators of adversity in childhood and risk of homelessness and point to the importance of early intervention efforts. Consistent with the extant research literature, mental health problems also appear to be associated with homelessness, highlighting the potentially complex service needs of this population.", "Health care generated data have become an important source for clinical and genomic research. Often, investigators create and iteratively refine phenotype algorithms to achieve high positive predictive values (PPVs) or sensitivity, thereby identifying valid cases and controls. These algorithms achieve the greatest utility when validated and shared by multiple health care systems.Materials and Methods We report the current status and impact of the Phenotype KnowledgeBase (PheKB, http://phekb.org), an online environment supporting the workflow of building, sharing, and validating electronic phenotype algorithms. We analyze the most frequent components used in algorithms and their performance at authoring institutions and secondary implementation sites. As of June 2015, PheKB contained 30 finalized phenotype algorithms and 62 algorithms in development spanning a range of traits and diseases. Phenotypes have had over 3500 unique views in a 6-month period and have been reused by other institutions. International Classification of Disease codes were the most frequently used component, followed by medications and natural language processing. Among algorithms with published performance data, the median PPV was nearly identical when evaluated at the authoring institutions (n = 44; case 96.0%, control 100%) compared to implementation sites (n = 40; case 97.5%, control 100%). These results demonstrate that a broad range of algorithms to mine electronic health record data from different health systems can be developed with high PPV, and algorithms developed at one site are generally transportable to others. By providing a central repository, PheKB enables improved development, transportability, and validity of algorithms for research-grade phenotypes using health care generated data.", "This study explored demographic influences on veterans' reports of homelessness or imminent risk of homelessness with a particular focus on gender. We analyzed data for a cohort of veterans who responded to the U.S. Department of Veterans Affairs (VA), Veterans Health Administration (VHA) universal screener for homelessness and risk during a 3-month period. Multinomial mixed effects models-stratified by gender-predicted veterans' reports of homelessness or risk based on age, race, marital status, and receipt of VA compensation. The proportion of positive screens-homelessness or risk-was 2.7% for females and 1.7% for males. Women more likely to report being at risk of homelessness were aged 35 to 54 years, Black, and unmarried; those more likely to experience homelessness were Black and unmarried. Among male veterans, the greatest predictors of both homelessness and risk were Black race and unmarried status. Among both genders, receiving VA disability compensation was associated with lesser odds of being homeless or at risk. The findings describe the current population of veterans using VHA health care services who may benefit from homelessness prevention or intervention services, identify racial differences in housing stability, and distinguish subpopulations who may be in particular need of intervention. Interventions to address these needs are described." ]
Endogenous retroviruses and their products in innate immune responses	About 8% of our genome is composed of sequences with viral origin, namely human Endogenous Retroviruses (HERVs). HERVs are relics of ancient infections that affected the primates' germ line along the last 100 million of years, and became stable elements at the interface between self and foreign DNA. Intriguingly, HERV co-evolution with the host led to the domestication of activities previously devoted to the retrovirus life cycle, providing novel cellular functions. For example, selected HERV envelope proteins have been coopted for pregnancy-related purposes, and proviral Long Terminal Repeats participate in the transcriptional regulation of various cellular genes. Given the HERV persistence in the host genome and its basal expression in most healthy tissues, it is reasonable that human defenses should prevent HERV-mediated immune activation. Despite this, HERVs and their products (including RNA, cytosolic DNA, and proteins) are still able to modulate and be influenced by the host immune system, fascinatingly suggesting a central role in the evolution and functioning of the human innate immunity. Indeed, HERV sequences had been major contributors in shaping and expanding the interferon network, dispersing inducible genes that have been occasionally domesticated in various mammalian lineages. Also the HERV integration within or near to genes encoding for critical immune factors has been shown to influence their activity, or to be responsible for their polymorphic variation in the human population, such as in the case of an HERV-K(HML10) provirus in the major histocompatibility complex region. In addition, HERV expressed products have been shown to modulate innate immunity effectors, being therefore often related on the one side to inflammatory and autoimmune disorders, while on the other side to the control of excessive immune activation through their immunosuppressive properties. Finally, HERVs have been proposed to establish a protective effect against exogenous infections. The present review summarizes the involvement of HERVs and their products in innate immune responses, describing how their intricate interplay with the first line of human defenses can actively contribute either to the host protection or to his damage, implying a subtle balance between the persistence of HERV expression and the maintenance of a basal immune alert.	[ "Human endogenous retroviruses (HERVs) are relics of ancient infections accounting for about the 8% of our genome. Despite their persistence in human DNA led to the accumulation of mutations, HERVs are still contributing to the human transcriptome, and a growing number of findings suggests that their expression products may have a role in various diseases. Among HERV products, the envelope proteins (Env) are currently highly investigated for their pathogenic properties, which could likely be participating to several disorders with complex etiology, particularly in the contexts of autoimmunity and cancer. In fact, HERV Env proteins have been shown, on the one side, to trigger both innate and adaptive immunity, prompting inflammatory, cytotoxic and apoptotic reactions; and, on the other side, to prevent the immune response activation, presenting immunosuppressive properties and acting as immune downregulators. In addition, HERV Env proteins have been shown to induce abnormal cell-cell fusion, possibly contributing to tumor development and metastasizing processes. Remarkably, even highly defective HERV env genes and alternative env splicing variants can provide further mechanisms of pathogenesis. A well-known example is the HERV-K(HML2) env gene that, depending on the presence or the absence of a 292-bp deletion, can originate two proteins of different length (Np9 and Rec) proposed to have oncogenic properties. The understanding of their involvement in complex pathological disorders made HERV Env proteins potential targets for therapeutic interventions. Of note, a monoclonal antibody directed against a HERV-W Env is currently under clinical trial as therapeutic approach for multiple sclerosis, representing the first HERV-based treatment. The present review will focus on the current knowledge of the HERV Env expression, summarizing its role in human physiology and its possible pathogenic effects in various cancer and autoimmune disorders. It moreover analyzes HERV Env possible exploitation for the development of innovative therapeutic strategies.", "Endogenous retroviruses (ERVs) are an inherited part of the eukaryotic genomes, and represent approximately 400,000 loci in the human genome. Human endogenous retroviruses (HERVs) can be divided into distinct families, composed of phylogenetically related but structurally heterogeneous elements. The majority of HERVs are silent in most physiological contexts, whereas a significant expression is observed in pathological contexts, such as cancers. Owing to their repetitive nature, few of the active HERV elements have been accurately identified. In addition, there are no criteria defining the active promoters among HERV long-terminal repeats (LTRs). Hence, it is difficult to understand the HERV (de)regulation mechanisms and their implication on the physiopathology of the host. We developed a microarray to specifically detect the LTR-containing transcripts from the HERV-H, HERV-E, HERV-W and HERV-K(HML-2) families. HERV transcriptome was analyzed in the placenta and seven normal/tumoral match-pair samples. We identified six HERV-W loci overexpressed in testicular cancer, including a usually placenta-restricted transcript of ERVWE1. For each locus, specific overexpression was confirmed by quantitative RT-PCR, and comparison of the activity of U3 versus U5 regions suggested a U3-promoted transcription coupled with 5'R initiation. The analysis of DNA from tumoral versus normal tissue revealed that hypomethylation of U3 promoters in tumors is a prerequisite for their activation.", "Integration of retroviral DNA into a germ cell may lead to a provirus that is transmitted vertically to that host's offspring as an endogenous retrovirus (ERV). In humans, ERVs (HERVs) comprise about 8% of the genome, the vast majority of which are truncated and/or highly mutated and no longer encode functional genes. The most recently active retroviruses that integrated into the human germ line are members of the Betaretrovirus-like HERV-K (HML-2) group, many of which contain intact open reading frames (ORFs) in some or all genes, sometimes encoding functional proteins that are expressed in various tissues. Interestingly, this expression is upregulated in many tumors ranging from breast and ovarian tissues to lymphomas and melanomas, as well as schizophrenia, rheumatoid arthritis, and other disorders. No study to date has characterized all HML-2 elements in the genome, an essential step towards determining a possible functional role of HML-2 expression in disease. We present here the most comprehensive and accurate catalog of all full-length and partial HML-2 proviruses, as well as solo LTR elements, within the published human genome to date. Furthermore, we provide evidence for preferential maintenance of proviruses and solo LTR elements on gene-rich chromosomes of the human genome and in proximity to gene regions. Our analysis has found and corrected several errors in the annotation of HML-2 elements in the human genome, including mislabeling of a newly identified group called HML-11. HML-elements have been implicated in a wide array of diseases, and characterization of these elements will play a fundamental role to understand the relationship between endogenous retrovirus expression and disease.", "The capacity to integrate into the chromosomal DNA of germ-line cells has endowed retroviruses with the potential to be vertically transmitted from generation to generation and eventually become fixed in the genomes of the entire population. This has been independently accomplished by several ancient retroviruses that invaded the genomes of our early and more recent primate and hominoid ancestors. Some of the inherited elements then proliferated in the genome, resulting in a number of lineages with complex phylogenetic patterns. Although the vast majority of chromosomally integrated retroelements have suffered inactivating mutations and deletions, a significant impact on various aspects of human biology has been recently revealed and evidence for the present activity of at least one human endogenous retrovirus family continues to accumulate.", "The human genome comprises 8 % endogenous retroviruses (ERVs), the majority of which are defective due to deleterious mutations. Nonetheless, transcripts of ERVs are found in most tissues, and these transcripts could either be reverse transcribed to generate ssDNA or expressed to generate proteins. Thus, the expression of ERVs could produce nucleic acids or proteins with viral signatures, much like the pathogen-associated molecular patterns of exogenous viruses, which would enable them to be detected by the innate immune system. The activation of some pattern recognition receptors (PRRs) in response to ERVs has been described in mice and in the context of human autoimmune diseases. Here, we review the evidence for detection of ERVs by PRRs and the resultant activation of innate immune signalling. This is an emerging area of research within the field of innate antiviral immunity, showing how ERVs could initiate immune signalling pathways and might have implications for numerous inflammatory diseases.", "In contrast to the extraordinary body of knowledge gained over the past three decades on the virology, pathogenesis, and immunology of HIV-1 infection, innate sensors that detect HIV-1 had remained elusive until recently. By virtue of integration, retroviridae makes up a substantial portion of our genome. Thus, immune strategies that deal with endogenous retroviruses are, by necessity, those of self-preservation and not of virus elimination. Some of the principles of such strategies may also apply for defense against exogenous retroviruses including HIV-1. Here, I highlight several sensors that have recently been revealed to be capable of recognizing distinct features of HIV-1 infection, while taking into account the host-retrovirus relationship that converges on avoiding pathogenic inflammatory consequences.", "Retrotransposons including endogenous retroviruses and their solitary long terminal repeats (LTRs) compose >40% of the human genome. Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host functions is not known. Here we show that an LTR retrotransposon of ERV-9 human endogenous retrovirus located 40-70 kb upstream of the human fetal gamma- and adult beta-globin genes serves a long-range, host function. The ERV-9 LTR contains multiple CCAAT and GATA motifs and competitively recruits a high concentration of NF-Y and GATA-2 present in low abundance in adult erythroid cells to assemble an LTR/RNA polymerase II complex. The LTR complex transcribes intergenic RNAs unidirectionally through the intervening DNA to loop with and modulate transcription factor occupancies at the far downstream globin promoters, thereby modulating globin gene switching by a competitive mechanism." ]
Hippocampal Activity Patterns Support Memory for Events with Overlapping Items and Contexts	Episodic memory is known to rely on the hippocampus, but how the hippocampus organizes different episodes to permit their subsequent retrieval remains controversial. One major area of debate hinges on a discrepancy between two hypothesized roles of the hippocampus: differentiating between similar events to reduce interference and assigning similar representations to events that share overlapping items and contextual information. Here, we used multivariate analyses of activity patterns measured with fMRI to characterize how the hippocampus distinguishes between memories based on similarity at the level of items and/or context. Hippocampal activity patterns discriminated between events that shared either item or context information but generalized across events that shared similar item-context associations. The current findings provide evidence that, whereas the hippocampus can reduce mnemonic interference by separating events that generalize along a single attribute dimension, overlapping hippocampal codes may support memory for events with overlapping item-context relations. This lends new insights into the way the hippocampus may balance multiple mnemonic operations in adaptively guiding behavior.	[ "The United States National Institutes of Health (NIH) commit significant support to open-source data and software resources in order to foment reproducibility in the biomedical imaging sciences. Here, we report and evaluate a recent product of this commitment: Advanced Neuroimaging Tools (ANTs), which is approaching its 2.0 release. The ANTs open source software library consists of a suite of state-of-the-art image registration, segmentation and template building tools for quantitative morphometric analysis. In this work, we use ANTs to quantify, for the first time, the impact of similarity metrics on the affine and deformable components of a template-based normalization study. We detail the ANTs implementation of three similarity metrics: squared intensity difference, a new and faster cross-correlation, and voxel-wise mutual information. We then use two-fold cross-validation to compare their performance on openly available, manually labeled, T1-weighted MRI brain image data of 40 subjects (UCLA's LPBA40 dataset). We report evaluation results on cortical and whole brain labels for both the affine and deformable components of the registration. Results indicate that the best ANTs methods are competitive with existing brain extraction results (Jaccard=0.958) and cortical labeling approaches. Mutual information affine mapping combined with cross-correlation diffeomorphic mapping gave the best cortical labeling results (Jaccard=0.669±0.022). Furthermore, our two-fold cross-validation allows us to quantify the similarity of templates derived from different subgroups. Our open code, data and evaluation scripts set performance benchmark parameters for this state-of-the-art toolkit. This is the first study to use a consistent transformation framework to provide a reproducible evaluation of the isolated effect of the similarity metric on optimal template construction and brain labeling.", "Recent functional imaging work supports the view that item and relational memory depend upon distinct encoding operations within the medial temporal lobe. Specifically, emerging findings demonstrate that the level of engagement of perirhinal cortex predicts later memory for individual items, whereas the level of hippocampal processing correlates with later relational memory, or recovery of additional episodic details. Furthermore, recent functional magnetic resonance imaging evidence in humans suggests that medial temporal lobe cortical input structures, the perirhinal and posterior parahippocampal cortices, differentially participate in the encoding of objects and their context, providing domain-specific input to the hippocampus. Taken together, these data help to construct a working model of how distinct medial temporal lobe structures participate in episodic memory formation with domain-general relational binding mechanisms supported by the hippocampus and provide emerging evidence for domain-specificity within the perirhinal and parahippocampal cortices.", "The episodic memory system enables accurate retrieval while maintaining flexibility by representing both specific episodes and generalizations across events. Although theories suggest that the hippocampus (HPC) is dedicated to represent specific episodes while the medial prefrontal cortex (MPFC) generalizes, other accounts posit that HPC can also integrate related memories. Here we use high-resolution functional magnetic resonance imaging in humans to examine how representations of memory elements change to either differentiate or generalize across related events. We show that while posterior HPC and anterior MPFC maintain distinct memories for individual events, anterior HPC and posterior MPFC integrate across memories. Integration is particularly likely for established memories versus those encoded simultaneously, highlighting the greater impact of prior knowledge on new encoding. We also show dissociable coding signatures in ventrolateral PFC, a region previously implicated in interference resolution. These data highlight how memory elements are represented to simultaneously promote generalization across memories and protect from interference.", "It is widely believed that the path to early and effective treatment for Alzheimer's disease (AD) requires the development of early diagnostic markers that are both sensitive and specific. To this aim, using longitudinal study designs, we and others have examined magnetic resonance imaging (MRI), 2-fluoro-2-deoxy-d-glucose-positron emission tomography (FDG/PET), and cerebrospinal fluid (CSF) biomarkers in cognitively normal elderly (NL) subjects and in patients with mild cognitive impairment (MCI). Such investigations have led to the often replicated findings that structural evidence of hippocampal atrophy as determined by MRI, as well as metabolic evidence from FDG-PET scan of hippocampal damage, predicts the conversion from MCI to AD. In this article we present a growing body of evidence of even earlier diagnosis. Brain pathology can be detected in NL subjects and used to predict future transition to MCI. This prediction is enabled by examinations revealing reduced glucose metabolism in the hippocampal formation (hippocampus and entorhinal cortex [EC]) as well as by the rate of medial temporal lobe atrophy as determined by MRI. However, neither regional atrophy nor glucose metabolism reductions are specific for AD. These measures provide secondary not primary evidence for AD. Consequently, we will also summarize recent efforts to improve the diagnostic specificity by combining imaging with CSF biomarkers and most recently by evaluating amyloid imaging using PET. We conclude that the combined use of conventional imaging, that is MRI or FDG-PET, with selected CSF biomarkers incrementally contributes to the early and specific diagnosis of AD. Moreover, selected combinations of imaging and CSF biomarkers measures are of importance in monitoring the course of AD and thus relevant to evaluating clinical trials.", "The present paper describes a comprehensive protocol for manual tracing of the set of brain regions comprising the medial temporal lobe (MTL): amygdala, hippocampus, and the associated parahippocampal regions (perirhinal, entorhinal, and parahippocampal proper). Unlike most other tracing protocols available, typically focusing on certain MTL areas (e.g., amygdala and/or hippocampus), the integrative perspective adopted by the present tracing guidelines allows for clear localization of all MTL subregions. By integrating information from a variety of sources, including extant tracing protocols separately targeting various MTL structures, histological reports, and brain atlases, and with the complement of illustrative visual materials, the present protocol provides an accurate, intuitive, and convenient guide for understanding the MTL anatomy. The need for such tracing guidelines is also emphasized by illustrating possible differences between automatic and manual segmentation protocols. This knowledge can be applied toward research involving not only structural MRI investigations but also structural-functional colocalization and fMRI signal extraction from anatomically defined ROIs, in healthy and clinical groups alike.", "Everyday behaviors require a high degree of flexibility, in which prior knowledge is applied to inform behavior in new situations. Such flexibility is thought to be supported in part by memory integration, a process whereby related memories become interconnected in the brain through recruitment of overlapping neuronal populations. Recent advances in cognitive and behavioral neuroscience highlight the importance of a hippocampal-medial prefrontal circuit in memory integration. Emerging evidence suggests that abstracted representations in medial prefrontal cortex guide reactivation of related memories during new encoding events, thus promoting hippocampal integration of related experiences. Moreover, recent work indicates that integrated memories are called upon during novel situations to facilitate a host of behaviors, from spatial navigation to imagination.", "In the early 1970s, Andersen and colleagues proposed that the principal excitatory pathways of the hippocampal formation were organized in a lamellar fashion. This proposition, based heavily on the physiological studies of the proponents, indicated that \"a point source of entorhinal activity projects its impulses through the four membered pathway (of the hippocampal formation) along a slice or lamella, of hippocampal tissue oriented normally to the alvear surface\" [Anderson P., Bliss V.P. and Skrede K. K. (1971) Expl Brain Res. 13, 222-238] and perpendicular to the long axis of the hippocampus. Andersen et al. further suggested that, \"By means of this lamellar organization, small strips of the hippocampal cortex may operate as independent functional units, although excitatory and inhibitory transverse connections may modify the behavior of neighboring lamellae.\" The \"lamellar hypothesis\" of hippocampal anatomical organization has had tremendous influence on the conceptualization of hippocampal information processing and was largely responsible for prompting the establishment of the in vitro hippocampal slice technology. While the \"lamellar hypothesis\" was consistent with the known neuroanatomy, subsequent neuroanatomical investigations, using a variety of modern tracing techniques, have invariably demonstrated that all of the major hippocampal projections, except for those arising from the granule cells of the dentate gyrus, are much more divergent than would be consistent with a strict interpretation of the lamellar hypothesis. This has become particularly clear in ongoing studies of the intrinsic hippocampal projections using the recently introduced anterograde tracer, Phaseolus vulgaris leucoagglutinin. Citing the conclusions from several papers dealing with the anatomical organization of the hippocampal formation and using examples from recent Phaseolus vulgaris leucoagglutinin mapping studies, the following are demonstrated. (1) That the major hippocampal projections are as extensive and highly organized in the long or septotemporal axis of the hippocampus as in the transverse axis. (2) That at least some of the hippocampal projections, such as the associational projections arising from the dentate gyrus, appear to be specifically organized to integrate distant levels of the hippocampal formation. (3) That the physiological data of Anderson et al. can be re-interpreted in the light of these new anatomical data to show how the stimulation and recording protocols used at the time would, in fact, generate the appearance of a lamellar organization. It is concluded that it is heuristically most reasonable to consider the hippocampal formation as a three-dimensional cortical region with important information processing taking place in both the transverse and long axes.(ABSTRACT TRUNCATED AT 400 WORDS)" ]
Post-translational modifications of human immunodeficiency virus proteins.	Human immunodeficiency virus (HIV) relies heavily on the host cellular machinery for production of viral progeny. To exploit cellular proteins for replication and to overcome host factors with antiviral activity, HIV has evolved a set of regulatory and accessory proteins to shape an optimized environment for its replication and to facilitate evasion from the immune system. Several cellular pathways are hijacked by the virus to modulate critical steps during the viral life cycle. Thereby, post-translational modifications (PTMs) of viral and cellular proteins gain increasingly attention as modifying enzymes regulate virtually every step of the viral replication cycle. This review summarizes the current knowledge of HIV-host interactions influenced by PTMs with a special focus on acetylation, ubiquitination, and phosphorylation of proteins linked to cellular signaling and viral replication. Insights into these interactions are surmised to aid development of new intervention strategies.	[ "The human immunodeficiency virus types 1 and 2 (HIV-1 and HIV-2) Tat proteins are related transcriptional activators whose effects are likely to be mediated by a cellular factor. Using an in vitro kinase assay, we have shown that the Tat protein of HIV-2 and the activation domain of the Tat protein of HIV-1 specifically bind to a cellular protein kinase. Mutations in Tat that abolish transactivation activity in vivo abrogate the ability of the mutants to bind to the kinase in vitro. This is the first demonstration of a cellular factor that binds to Tat that is specific for a functional activation domain of Tat and that displays a biochemical activity. Additionally, we show that the Tat protein of HIV-2 serves as a substrate of the kinase in vitro. Consistent with the in vitro results, the Tat protein of HIV-2 interacts with a cellular kinase in HIV-2 Tat-transfected cells and is phosphorylated in vivo. These results suggest that a cellular serine/threonine kinase may act as a mediator of Tat function.", "Human immunodeficiency virus type 1 (HIV-1) has evolved various measures to counter the host cell's innate antiviral response during the course of infection. Interferon (IFN)-stimulated gene products are produced following HIV-1 infection to limit viral replication, but viral proteins and RNAs counteract their effect. One such mechanism is specifically directed against the IFN-induced Protein Kinase PKR, which is centrally important to the cellular antiviral response. In the presence of viral RNAs, PKR is activated and phosphorylates the translation initiation factor eIF2α. This shuts down the synthesis of both host and viral proteins, allowing the cell to mount an effective antiviral response. PACT (protein activator of PKR) is a cellular protein activator of PKR, primarily functioning to activate PKR in response to cellular stress. Recent studies have indicated that during HIV-1 infection, PACT's normal cellular function is compromised and that PACT is unable to activate PKR. Using various reporter systems and in vitro kinase assays, we establish in this report that interactions between PACT, ADAR1 and HIV-1-encoded Tat protein diminish the activation of PKR in response to HIV-1 infection. Our results highlight an important pathway by which HIV-1 transcripts subvert the host cell's antiviral activities to enhance their translation.", "Viral protein R (Vpr) of human immunodeficiency virus type 1 (HIV-1) is a small accessory protein that regulates nuclear import of the viral preintegration complex and facilitates infection of nondividing cells, such as macrophages. Studies demonstrated that a fraction of Vpr molecules is phosphorylated in the virions and in HIV-1-infected cells, but the role of phosphorylation in nuclear import activity of Vpr has not been established. We found that Vpr is phosphorylated predominantly on the serine residue in position 79, and mutations affecting Vpr phosphorylation significantly attenuated viral replication in macrophages, but not in activated T lymphocytes or cell lines. The replication defect was mapped by polymerase chain reaction analysis to the step of nuclear import. These results suggest that phosphorylation of Vpr regulates its activity in the nuclear import of the HIV-1 preintegration complex.", "Trans-activation response (TAR) RNA-binding protein (TRBP) is a cellular protein that binds to the human immunodeficiency virus-1 (HIV-1) TAR element RNA. It has two double-stranded RNA binding domains (dsRBDs), but only one is functional for TAR binding. TRBP interacts with the interferon-induced protein kinase R (PKR) and inhibits its activity. We used the yeast two-hybrid assay to map the interaction sites between the two proteins. We show that TRBP and PKR-N (178 first amino acids of PKR) interact with PKR wild type and inhibit the PKR-induced yeast growth defect in this assay. We characterized two independent PKR-binding sites in TRBP. These sites are located in each dsRBD in TRBP, indicating that PKR-TRBP interaction does not require the RNA binding activity present only in dsRBD2. TRBP and its fragments that interact with PKR reverse the PKR-induced suppression of HIV-1 long terminal repeat expression. In addition, TRBP activates the HIV-1 long terminal repeat expression to a larger extent than the addition of each domain. These data suggest that TRBP activates gene expression in PKR-dependent and PKR-independent manners.", "Translation is a regulated process and is pivotal to proper cell growth and homeostasis. All retroviruses rely on the host translational machinery for viral protein synthesis and thus may be susceptible to its perturbation in response to stress, co-infection, and/or cell cycle arrest. HIV-1 infection arrests the cell cycle in the G2/M phase, potentially disrupting the regulation of host cell translation. In this study, we present evidence that HIV-1 infection downregulates translation in lymphocytes, attributable to the cell cycle arrest induced by the HIV-1 accessory protein Vpr. The molecular basis of the translation suppression is reduced accumulation of the active form of the translation initiation factor 4E (eIF4E). However, synthesis of viral structural proteins is sustained despite the general suppression of protein production. HIV-1 mRNA translation is sustained due to the distinct composition of the HIV-1 ribonucleoprotein complexes. RNA-coimmunoprecipitation assays determined that the HIV-1 unspliced and singly spliced transcripts are predominantly associated with nuclear cap binding protein 80 (CBP80) in contrast to completely-spliced viral and cellular mRNAs that are associated with eIF4E. The active translation of the nuclear cap binding complex (CBC)-bound viral mRNAs is demonstrated by ribosomal RNA profile analyses. Thus, our findings have uncovered that the maintenance of CBC association is a novel mechanism used by HIV-1 to bypass downregulation of eIF4E activity and sustain viral protein synthesis. We speculate that a subset of CBP80-bound cellular mRNAs contribute to recovery from significant cellular stress, including human retrovirus infection.", "Higher eukaryotic organisms have a variety of specific and nonspecific defense mechanisms against viral invaders. In animal cells, viral replication may be limited through the decrease in translation. Some viruses, however, have evolved mechanisms that counteract the response of the host. We report that infection by HIV-1 triggers acute decrease in translation. The human protein kinase GCN2 (eIF2AK4) is activated by phosphorylation upon HIV-1 infection in the hours following infection. Thus, infection by HIV-1 constitutes a stress that leads to the activation of GCN2 with a resulting decrease in protein synthesis. We have shown that GCN2 interacts with HIV-1 integrase (IN). Transfection of IN in amino acid-starved cells, where GCN2 is activated, increases the protein synthesis level. These results point to an as yet unknown role of GCN2 as an early mediator in the cellular response to HIV-1 infection, and suggest that the virus is able to overcome the involvement of GCN2 in the cellular response by eliciting methods to maintain protein synthesis.", "The double stranded RNA (dsRNA)-activated protein kinase PKR is a ubiquitously expressed serine/threonine protein kinase that is induced by interferon and activated by dsRNA, cytokine, growth factor and stress signals. It is essential for cells to respond adequately to different stresses including growth factor deprivation, products of the inflammatory response (TNF) and bacterial (lipopolysaccharide) and viral (dsRNA) products. As a vital component of the cellular antiviral response pathway, PKR is autophosphorylated and activated on binding to dsRNA. This results in inhibition of protein synthesis via the phosphorylation of eIF2alpha and also induces transcription of inflammatory genes by PKR-dependent signaling of the activation of different transcription factors. Along with RNaseL, PKR constitutes the antiviral arm of a group of mammalian stress response proteins that have counterparts in yeast. What began as adaptation to amino acid deprivation and sensing unfolded proteins in the endoplasmic reticulum has evolved into a family of sophisticated mammalian stress response proteins able to mediate cellular responses to both physical and biological stress.", "Phosphorylation of the alpha subunit of eukaryotic initiation factor-2 (eIF-2) is a well characterized mechanism regulating protein synthesis. Viral and cellular proteins have been identified that regulate the activity of the eIF-2alpha kinases. The regulatory protein, K3L, from vaccinia virus is homologous to the amino terminus of eIF-2alpha and is thought to inhibit the activity of the double-stranded RNA-dependent kinase suppressing the antiviral mechanism mediated by this kinase. We investigated whether K3L can inhibit the activity of the yeast eIF-2alpha kinase GCN2. Expression of K3L protein in yeast reduced the level of eIF-2alpha phosphorylation by GCN2 and blocked the stimulation of the general amino acid control pathway in response to starvation conditions. Accompanying in vitro studies showed that recombinant K3L protein reduced GCN2 autophosphorylation and phosphorylation eIF-2alpha. In agreement with the hypothesis that K3L inhibits eIF-2alpha kinases by functioning as a pseudosubstrate, we observed that K3L directly interacted with the kinase catalytic domain of GCN2. Together, these results indicate that K3L is a specific inhibitor of eIF-2alpha kinases from mammals and yeast and suggest that the kinases contain common structural features important for recognition of their substrate eIF-2alpha.", "The interferon (IFN)-induced, dsRNA-dependent serine/threonine protein kinase, PKR, plays a key regulatory role in the IFN-mediated anti-viral response by blocking translation in the infected cell by phosphorylating the alpha subunit of elongation factor 2 (eIF2). The human immunodeficiency virus type 1 (HIV-1) evades the anti-viral IFN response through the binding of one of its major transcriptional regulatory proteins, Tat, to PKR. HIV-1 Tat acts as a substrate homologue for the enzyme, competing with eIF2alpha, and inhibiting the translational block. It has been shown that during the interaction with PKR, Tat becomes phosphorylated at three residues: serine 62, threonine 64 and serine 68. We have investigated the effect of this phosphorylation on the function of Tat in viral transcription. HIV-1 Tat activates transcription elongation by first binding to TAR RNA, a stem-loop structure found at the 5' end of all viral transcripts. Our results showed faster, greater and stronger binding of Tat to TAR RNA after phosphorylation by PKR. We have investigated the effect of phosphorylation on Tat-mediated transactivation. Our results showed faster, greater and stronger binding of Tat to TAR RNA after phosphorylation by PKR. In vitro phosphorylation experiments with a series of bacterial expression constructs carrying the wild-type tat gene or mutants of the gene with alanine substitutions at one, two, or all three of the serine/threonine PKR phosphorylation sites, showed that these were subject to different levels of phosphorylation by PKR and displayed distinct kinetic behaviour. These results also suggested a cooperative role for the phosphorylation of S68 in conjunction with S62 and T64. We examined the effect of phosphorylation on Tat-mediated transactivation of the HIV-1 LTR in vivo with a series of analogous mammalian expression constructs. Co-transfection experiments showed a gradual reduction in transactivation as the number of mutated phosphorylation sites increased, and a 4-fold decrease in LTR transactivation with the Tat triple mutant that could not be phosphorylated by PKR. Furthermore, the transfection data also suggested that the presence of S68 is necessary for optimal Tat-mediated transactivation. These results support the hypothesis that phosphorylation of Tat may be important for its function in HIV-1 LTR transactivation.", "Infection of human cell with human immunodeficiency virus type-1 (HIV-1) was suppressed by cellular genetic factor(s) at reverse transcription step. Although same amount of virus adsorbed on both cells, small amount of HIV-1 (IIIB strain) infected HeLa (MAGI/CCR5) cell, while large amount of HIV-1 infected HOS (GHOST/CXCR4) cell. Regulation of virus replication at postentry level by cellular factor(s) had an important role for low efficiency of HIV-1 infection to MAGI/CCR5 cell. Provirus DNA formation in MAGI/CCR5 cell was less efficient than in GHOST/CXCR4 cell. Once GHOST/CXCR4 cell was fused with MAGI/CCR5 cell, susceptibility against HIV-1 decreased. Further, HIV-1 reverse transcriptase (RT) activity was strongly inhibited by cytosolic protein, derived from MAGI/CCR5 cell, in vitro. This research cleared a certain human cell genetically carries some factor(s) which inhibits the activity of HIV-1 RT." ]
Effects of phasic alerting on multisensory temporal processing	The relationship between attention and multisensory integration has attracted the attention of many researchers but remains a topic of debate. As a mechanism that regulates the intensity of attention, little is known regarding whether and how phasic alerting affects multisensory perception. Three experiments and warning cues were employed to investigate the influence of phasic alerting on multisensory temporal processing. Experiments 1 and 2 used a temporal order judgement task and a simultaneity judgement task with audiovisual target stimuli presented at varying stimulus onset asynchronies. Experiment 3 further adopted a dual task to generate a new estimate of participants' performance. Although these tasks differ in terms of the required cognitive mechanisms, decreased just noticeable difference scores in trials with warning cues consistently indicated that participants under phasic alerting had enhanced multisensory temporal precision. The point of subjective simultaneity values differed among the three tasks, suggesting that the influence of phasic alerting on perceptual deviation might be modulated by specific task demands. Experiment 4 adopted a strict method to verify that the mechanisms by which warning cues facilitate multisensory temporal precision are most likely transient general arousal rather than temporal expectancy. There is a close relationship between multisensory integration and some neurodevelopmental disorders. Considering that phasic alerting may heighten attentional capacity, future research could explore the potential medical interventions for the patients with relatively limited attention resources.	[ "From language to motor control, efficient integration of information from different sensory modalities is necessary for maintaining a coherent interaction with the environment. While a number of training studies have focused on training perceptual and cognitive function, only very few are specifically targeted at improving multisensory processing. Discrimination of temporal order or coincidence is a criterion used by the brain to determine whether cross-modal stimuli should be integrated or not. In this study we trained older adults to judge the temporal order of visual and auditory stimuli. We then tested whether the training had an effect in reducing susceptibility to a multisensory illusion, the sound induced flash illusion. Improvement in the temporal order judgement task was associated with a reduction in susceptibility to the illusion, particularly at longer Stimulus Onset Asynchronies, in line with a more efficient multisensory processing profile. The present findings set the ground for more broad training programs aimed at improving older adults׳ cognitive performance in domains in which efficient temporal integration across the senses is required.", "Information from the different senses is seamlessly integrated by the brain in order to modify our behaviors and enrich our perceptions. It is only through the appropriate binding and integration of information from the different senses that a meaningful and accurate perceptual gestalt can be generated. Although a great deal is known about how such cross-modal interactions influence behavior and perception in the adult, there is little knowledge as to the impact of aging on these multisensory processes. In the current study, we examined the speed of discrimination responses of aged and young individuals to the presentation of visual, auditory or combined visual-auditory stimuli. Although the presentation of multisensory stimuli speeded response times in both groups, the performance gain was significantly greater in the aged. Most strikingly, multisensory stimuli restored response times in the aged to those seen in young subjects to the faster of the two unisensory stimuli (i.e., visual). The current results suggest that despite the decline in sensory processing that accompanies aging, the use of multiple sensory channels may represent an effective compensatory strategy to overcome these unisensory deficits.", "Saccadic reaction time (SRT) to a visual stimulus tends to be faster when an auditory and/or somatosensory stimulus is presented in close temporal or spatial proximity, even when participants are instructed to ignore the accessory input (focused attention task). The time course of SRT as a function of stimulus onset asynchrony (SOA) is consistent with the time-window-of-integration (TWIN) model assuming a peripheral stage of parallel processing in separate sensory channels followed by a secondary stage of multisensory integration. TWIN has been shown to account for effects of the spatial configuration of the stimuli, for the effect of increasing the number of nontargets presented together with the target, for a possible warning effect of the nontarget, for effects of increasing the intensity of the nontarget, and for the effect of background noise on multisensory integration. Moreover, it has been able to accommodate some effects of aging on multisensory integration. There is empirical support for TWIN's tenet of the separability between spatial and temporal factors on multisensory integration. Besides presenting many features of TWIN within the context of crossmodal interaction modeling efforts, some possible directions on how the TWIN framework could serve to elucidate the link between perception and action are shown.", "The most popular tasks with which to investigate the perception of subjective synchrony are the temporal order judgment (TOJ) and the simultaneity judgment (SJ). Here, we discuss a complementary approach-a dual-presentation (2x) SJ task-and focus on appropriate analysis methods for a theoretically desirable \"roving\" design. Two stimulus pairs are presented on each trial and the observer must select the most synchronous. To demonstrate this approach, in Experiment 1 we tested the 2xSJ task alongside TOJ, SJ, and simple reaction-time (RT) tasks using audiovisual stimuli. We interpret responses from each task using detection-theoretic models, which assume variable arrival times for sensory signals at critical brain structures for timing perception. All tasks provide similar estimates of the point of subjective simultaneity (PSS) on average, and PSS estimates from some tasks were correlated on an individual basis. The 2xSJ task produced lower and more stable estimates of model-based (and thus comparable) sensory/decision noise than the TOJ. In Experiment 2 we obtained similar results using RT, TOJ, ternary, and 2xSJ tasks for all combinations of auditory, visual, and tactile stimuli. In Experiment 3 we investigated attentional prior entry, using both TOJs and 2xSJs. We found that estimates of prior-entry magnitude correlated across these tasks. Overall, our study establishes the practicality of the roving dual-presentation SJ task, but also illustrates the additional complexity of the procedure. We consider ways in which this task might complement more traditional procedures, particularly when it is important to estimate both PSS and sensory/decisional noise.", "The notion of the temporal window of integration, when applied in a multisensory context, refers to the breadth of the interval across which the brain perceives two stimuli from different sensory modalities as synchronous. It maintains a unitary perception of multisensory events despite physical and biophysical timing differences between the senses. The boundaries of the window can be influenced by attention and past sensory experience. Here we examined whether task demands could also influence the multisensory temporal window of integration. We varied the stimulus onset asynchrony between simple, short-lasting auditory and visual stimuli while participants performed two tasks in separate blocks: a temporal order judgment task that required the discrimination of subtle auditory-visual asynchronies, and a reaction time task to the first incoming stimulus irrespective of its sensory modality. We defined the temporal window of integration as the range of stimulus onset asynchronies where performance was below 75% in the temporal order judgment task, as well as the range of stimulus onset asynchronies where responses showed multisensory facilitation (race model violation) in the reaction time task. In 5 of 11 participants, we observed audio-visual stimulus onset asynchronies where reaction time was significantly accelerated (indicating successful integration in this task) while performance was accurate in the temporal order judgment task (indicating successful segregation in that task). This dissociation suggests that in some participants, the boundaries of the temporal window of integration can adaptively recalibrate in order to optimize performance according to specific task demands.", "We examined whether the known noradrenergic attenuation of the alerting effect (the beneficial effect of a warning cue) results from an underlying effect of noradrenaline on temporal orienting (orienting toward a particular moment in time). Following a within-subjects, counterbalanced design, 10 healthy human volunteers received placebo, 200 microg clonidine or 1 mg guanfacine (alpha2 agonists) in three separate testing sessions. Subjects were scanned by fMRI while performing attentional orienting tasks containing spatially informative, temporally informative, non-informative or no cues. The alerting effect primarily activated left-lateralized prefrontal, premotor and parietal regions. Clonidine, but not guanfacine, impaired behavioural measures of the alerting effect while attenuating activity in the left temporo-parietal junction. Replicating previous results, the temporal orienting task activated left parietal and frontal cortex, while parietal cortex was activated bilaterally during spatial orienting. Of these networks, clonidine, but not guanfacine, attenuated left prefrontal cortex and insula activity during temporal orienting and attenuated right superior parietal cortex activity during spatial orienting,. To complement these neuroanatomical changes, clonidine produced selective behavioural effects on both temporal and spatial orienting. The anatomical dissociation between the effects of clonidine during temporal orienting versus alerting suggests that noradrenergic modulation of the alerting effect does not result only from an underlying effect on temporal orienting. Furthermore, we have demonstrated lateralized neuroanatomical substrates for the noradrenergic modulation of human attentional orienting in the spatial and temporal domains.", "In divided-attention tasks, responses are faster when two target stimuli are presented, and thus one is redundant, than when only a single target stimulus is presented. Raab (1962) suggested an account of this redundant-targets effect in terms of a race model in which the response to redundant target stimuli is initiated by the faster of two separate target detection processes. Such models make a prediction about the probability distributions of reaction times that is often called the race model inequality, and it is often of interest to test this prediction. In this article, we describe a precise algorithm that can be used to test the race model inequality and present MATLAB routines and a Pascal program that implement this algorithm.", "Recent research has demonstrated enhanced visual attention and visual perception in individuals with extensive experience playing action video games. These benefits manifest in several realms, but much remains unknown about the ways in which video game experience alters perception and cognition. In the present study, we examined whether video game players' benefits generalize beyond vision to multisensory processing by presenting auditory and visual stimuli within a short temporal window to video game players and non-video game players. Participants performed two discrimination tasks, both of which revealed benefits for video game players: In a simultaneity judgment task, video game players were better able to distinguish whether simple visual and auditory stimuli occurred at the same moment or slightly offset in time, and in a temporal-order judgment task, they revealed an enhanced ability to determine the temporal sequence of multisensory stimuli. These results suggest that people with extensive experience playing video games display benefits that extend beyond the visual modality to also impact multisensory processing.", "Intracranial recordings from three human subjects provide the first direct electrophysiological evidence for audio-visual multisensory processing in the human superior parietal lobule (SPL). Auditory and visual sensory inputs project to the same highly localized region of the parietal cortex with auditory inputs arriving considerably earlier (30 ms) than visual inputs (75 ms). Multisensory integration processes in this region were assessed by comparing the response to simultaneous audio-visual stimulation with the algebraic sum of responses to the constituent auditory and visual unisensory stimulus conditions. Significant integration effects were seen with almost identical morphology across the three subjects, beginning between 120 and 160 ms. These results are discussed in the context of the role of SPL in supramodal spatial attention and sensory-motor transformations.", "Enumeration of elements differs as a function of their range. Subitizing (quantities 1-4) is considered to be an accurate and quick process with reaction times minimally affected by the number of presented elements within its range. In contrast, small estimation (range of 5-9 elements exposed briefly) is a less precise linear process. Subitizing was consider to be a pre-attentive process for many years. However, recent studies found that when attentional resources were occupied elsewhere, the subitizing process was impaired. In the current study, we examined whether subitizing can be facilitated by improving engagement of attention. Specifically, brief alerting cues that increase attentional engagement were presented in half of the trials during enumeration tasks. In Experiment 1, participants were required to enumerate dots presented in random arrays within the subitizing or small estimation range. Alerting facilitated enumeration of quantities in the subitizing range, but not in the small estimation range. We suggested that the benefit of alerting on the subitizing process was achieved via enhancement of global processing, a process that was previously associated with both alerting and subitizing. In Experiment 2, we provided direct evidence for this hypothesis by demonstrating that when global processing was used for items in the small estimation range (i.e., presenting quantities in a canonical array), a subitizing-like pattern was revealed in quantities beyond the subitizing range." ]
what is the relationship between attention and effort?	Daniel Kahneman was not the first to suggest that attention and effort are closely associated, but his 1973 book	[ "Frontal midline theta rhythm (Fm theta), recognized as distinct theta activity on EEG in the frontal midline area, reflects mental concentration as well as meditative state or relief from anxiety. Attentional network in anterior frontal lobes including anterior cingulate cortex is suspected to be the generator of this activity, and the regulative function of the frontal neural network over autonomic nervous system (ANS) during cognitive process is suggested. However no studies have examined peripheral autonomic activities during Fm theta induction, and interaction of central and peripheral mechanism associated with Fm theta remains unclear. In the present study, a standard procedure of Zen meditation requiring sustained attention and breath control was employed as the task to provoke Fm theta, and simultaneous EEG and ECG recordings were performed. For the subjects in which Fm theta activities were provoked (six men, six women, 48% of the total subjects), peripheral autonomic activities were evaluated during the appearance of Fm theta as well as during control periods. Successive inter-beat intervals were measured from the ECG, and a recently developed method of analysis by Toichi et al. (J. Auton. Nerv. Syst. 62 (1997) 79-84) based on heart rate variability was used to assess cardiac sympathetic and parasympathetic functions separately. Both sympathetic and parasympathetic indices were increased during the appearance of Fm theta compared with control periods. Theta band activities in the frontal area were correlated negatively with sympathetic activation. The results suggest a close relationship between cardiac autonomic function and activity of medial frontal neural circuitry.", "An association between the liability to early onset alcoholism/substance abuse and a recently discovered dinucleotide repeat length polymorphism at the MAOA gene (MAOCA-1) was examined using polymerase chain reaction (PCR). A significant correlation between the presence/absence of the disorder and the length of the MAOCA-1 repeat was found in males, but not females, with \"long\" alleles (repeat length above 115 bp) associated with both increased risk for the disorder and lower age of onset of substance abuse. These preliminary data suggest that further exploration of the relationship between the MAOA gene and behavioral traits in an expanded sample is warranted.", "There is evidence for an association between polymorphisms of monoamine transporter genes and temperamental personality traits. Recent findings have shown that interaction of allelic variants of the different genes may contribute to the personality factors. We studied the association between temperamental personality dimensions measured with the Temperament and Character Inventory (TCI) and polymorphisms of the dopamine (DAT), norepinephrine (NET) and serotonin (5-HTT) transporter genes in 127 healthy Polish volunteers. There were no significant differences between means of TCI temperamental dimensions (novelty seeking, reward dependence, persistence and harm avoidance) and the transporter genes compared by ANOVA. There were some significant associations between genotypes and TCI subdimensions. Individuals carrying the A9/A9 DAT genotype have lower RD4 scores (dependence vs. independence) than A10/A10 individuals (3.0 +/- 1.4 vs. 3.5 +/- 1.3); p = 0.01. Examining 5-HTT gene promoter polymorphism, heterozygous individuals (l/s) and individuals with 44-bp deletion (s/s) scored significantly lower in the HA1 subdimension (anticipatory worry and pessimism vs. uninhibited optimism; 4.3 +/- 2.3 vs. 5.5 +/- 2.6) in comparison with individuals without deletion (l/l); p = 0.021. The NET transporter gene polymorphism showed no significant association with any of the temperamental TCI subdimensions.", "Noradrenergic locus coeruleus (LC) neurons were recorded in monkeys performing a visual discrimination task, and a computational model was developed addressing the role of the LC brain system in cognitive performance. Changes in spontaneous and stimulus-induced patterns of LC activity correlated closely with fluctuations in behavioral performance. The model explains these fluctuations in terms of changes in electrotonic coupling among LC neurons and predicts improved performance during epochs of high coupling and synchronized LC firing. Cross correlations of simultaneously recorded LC neurons confirmed this prediction, indicating that electrotonic coupling in LC may play an important role in attentional modulation and the regulation of goal-directed versus exploratory behaviors.", "Experiments were conducted to elucidate the role of the noradrenergic neurotransmitter system in arousal and the orienting of attention. Rhesus monkeys were trained to perform a peripherally cued, covert orienting task for juice reward, and their manual reaction times (RTs) to visual stimuli were measured. The effects of parenteral injections of the alpha-2 adrenergic agonists clonidine and guanfacine, and normal saline were compared on the covert task. We assessed 1) overall error rates, 2) the difference in RTs between validly and invalidly cued trials (validity effect), 3) the difference in RTs between neutral and no-cue trials (alerting effect), 4) target location (visual field), and 5) cue-target interval. Changes in noradrenaline levels produced by clonidine (and to a lesser extent guanfacine) significantly decreased the alerting effect, and lowered RTs to stimuli in the left visual field, but did not change the validity effect, suggesting that noradrenaline is involved in maintaining non-spatial, sensory readiness to external cues but not in the shifting of the attentional focus.", "We studied a large sample of male children from birth to adulthood to determine why some children who are maltreated grow up to develop antisocial behavior, whereas others do not. A functional polymorphism in the gene encoding the neurotransmitter-metabolizing enzyme monoamine oxidase A (MAOA) was found to moderate the effect of maltreatment. Maltreated children with a genotype conferring high levels of MAOA expression were less likely to develop antisocial problems. These findings may partly explain why not all victims of maltreatment grow up to victimize others, and they provide epidemiological evidence that genotypes can moderate children's sensitivity to environmental insults.", "The therapeutic effects of methylphenidate in the treatment of attention deficit disorder have been attributed to its ability to increase the synaptic concentration of dopamine by blocking the dopamine transporters. However, the levels of dopamine transporter blockade achieved by therapeutic doses of methylphenidate are not known. This study measured, for the first time, dopamine transporter occupancy by orally administered methylphenidate in the human brain and its rate of uptake in the brain. Positron emission tomography (PET) and [11C]cocaine were used to estimate dopamine transporter occupancies after different doses of oral methylphenidate in seven normal subjects (mean age=24 years, SD=7). In addition, the pharmacokinetics of oral methylphenidate were measured in the baboon brain through use of PET and [11C]methylphenidate administered through an orogastric tube. At 120 minutes after administration, oral methylphenidate produced a dose-dependent blockade of dopamine transporter; means=12% (SD= 4%) for 5 mg, 40% (SD=12%) for 10 mg, 54% (SD=5%) for 20 mg, 72% (SD=3%) for 40 mg, and 74% (SD=2%) for 60 mg. The estimated dose of oral methylphenidate required to block 50% of the dopamine transporter corresponded to 0.25 mg/kg. Oral methylphenidate did not reach peak concentration in brain until 60 minutes after its administration. Oral methylphenidate is very effective in blocking dopamine transporters, and at the weight-adjusted doses used therapeutically (0.3 to 0.6 mg/kg), it is likely to occupy more than 50% of the dopamine transporters. The time to reach peak brain uptake for oral methylphenidate in brain corresponds well with the reported time course to reach peak behavioral effects.", "Changes in pupil diameter that reflect effort and other cognitive factors are often interpreted in terms of the activity of norepinephrine-containing neurons in the brainstem nucleus locus coeruleus (LC), but there is little direct evidence for such a relationship. Here, we show that LC activation reliably anticipates changes in pupil diameter that either fluctuate naturally or are driven by external events during near fixation, as in many psychophysical tasks. This relationship occurs on as fine a temporal and spatial scale as single spikes from single units. However, this relationship is not specific to the LC. Similar relationships, albeit with delayed timing and different reliabilities across sites, are evident in the inferior and superior colliculus and anterior and posterior cingulate cortex. Because these regions are interconnected with the LC, the results suggest that non-luminance-mediated changes in pupil diameter might reflect LC-mediated coordination of neuronal activity throughout some parts of the brain.", "Current efforts to study the genetic underpinnings of higher brain functions have been lacking appropriate phenotypes to describe cognition. One of the problems is that many cognitive concepts for which there is a single word (e.g. attention) have been shown to be related to several anatomical networks. Recently, we have developed an Attention Network Test (ANT) that provides a separate measure for each of three anatomically defined attention networks. In this study we have measured the efficiency of neural networks related to aspects of attention using the ANT in a population of 200 adult subjects. We then examined genetic polymorphisms in four candidate genes (DRD4, DAT, COMT and MAOA) that have been shown to contribute to the risk of developing various psychiatric disorders where attention is disrupted. We find modest associations of several polymorphisms with the efficiency of executive attention but not with overall performance measures such as reaction time. These results suggest that genetic variation may underlie inter-subject variation in the efficiency of executive attention. This study also shows that genetic influences on executive attention may be specific to certain anatomical networks rather than affecting performance in a global or non-specific manner. Lastly, this study further validates the ANT as an endophenotypic assay suitable for assessing how genes influence certain anatomical networks that may be disrupted in various psychiatric disorders.", "In non-clinical low-risk populations 15% of infants show disorganized attachment behavior(1,2) with their caregivers in the Strange Situation,(3) a mildly stressful laboratory procedure testing infants' ability to cope with separation anxiety. Disorganization of early attachment has been primarily ascribed to inadequate parenting,(2,4,5) and has been associated with childhood behavior problems(6,7)and adolescent psychopathological tendencies.(5) We have recently reported an association between the DRD4 exon III 48 basepair repeat polymorphism and disorganization of infants' attachment behavior towards their mother in a low-social-risk group of 1-year-old infants:(8) the risk for disorganized attachment among infants carrying the 7-repeat allele was fourfold. Here we report further evidence for the involvement of the dopamine D4 receptor gene in attachment disorganization. The same group of infants was genotyped for the functional -521 C/T single nucleotide polymorphism (SNP) in the upstream regulatory region of the DRD4 gene(9) in order to test the association with attachment disorganization both alone and in interaction with the DRD4 exon III 7-repeat allele. While the -521 C/T genotype itself had no effect on attachment status (chi(2) = 0.41, df = 2, P = 0.82), there was an interaction between the structural 48-bp repeat polymorphism and the -521 C/T promoter polymorphism: the association between disorganized attachment and the 7-repeat allele was enhanced in the presence of the -521 T allele (chi(2) = 6.61 and 6.67, df = 1, P < 0.025 for CT and TT genotypes, respectively). In the presence of both risk alleles the odds ratio for disorganized attachment increased tenfold. This result supports our previous postulation that the DRD4 gene plays a role in the development of attachment behavior in low-risk, non-clinical populations." ]
Effect of Methylphenidate on In Vitro Autoradiography in Adolescent Male Rats	Methylphenidate (MP) is a widely prescribed psychostimulant used to treat attention deficit hyperactivity disorder. Previously, we established a drinking paradigm to deliver MP to rats at doses that result in pharmacokinetic profiles similar to treated patients. In the present study, adolescent male rats were assigned to one of three groups: control (water), low-dose MP (LD; 4/10 mg/kg), and high dose MP (HD; 30/60 mg/kg). Following 3 months of treatment, half of the rats in each group were euthanized, and the remaining rats received only water throughout a 1-month-long abstinence phase. In vitro autoradiography using [	[ "Methylphenidate is the first-choice treatment for attention-deficit/hyperactivity disorder (ADHD), but its mechanism of action is incompletely understood. The cognitive effects of methylphenidate have been extensively studied, but little is known about its effects on spontaneous social behavior. During adolescence, rats display a characteristic, highly vigorous form of social behavior, termed social play behavior, which is of critical importance for social and cognitive development. We investigated the neurobehavioral mechanisms by which methylphenidate affects social play behavior in rats. Methylphenidate (0.3-3.0 mg/kg, s.c. or p.o.) abolished social play behavior, without altering general social interest. This effect of methylphenidate did not depend upon the baseline level of social play and was not secondary to changes in locomotion. Furthermore, the play-suppressant effect of methylphenidate was not subject to tolerance or sensitization. Methylphenidate blocked both the initiation to play and the responsivity to play initiation. The effect of methylphenidate was mimicked by the noradrenaline reuptake inhibitor atomoxetine, which is also used for the treatment of ADHD, and was blocked by an alpha-2 adrenoceptor antagonist. In addition, combined administration of subeffective doses of methylphenidate and atomoxetine suppressed social play. However, blockade of alpha-1 adrenoceptors, beta-adrenoceptors, or dopamine receptors did not alter the effect of methylphenidate. These data show that methylphenidate selectively blocks the most vigorous part of the behavioral repertoire of adolescent rats through a noradrenergic mechanism. We suggest that the effect of methylphenidate on social play is a reflection of its therapeutic effect in ADHD, that is, improved behavioral inhibition. However, given the importance of social play for development, these findings may also indicate an adverse side effect of methylphenidate.", "The effects of morphine on social play behavior in juvenile rats were investigated using sequential analysis. Social play behavior of 21-day-old rats treated with 1.0 mg/kg of morphine or saline was analyzed for 15 min. Frequencies and durations of measures of social play behavior, such as pinning, boxing/wrestling and following/chasing were significantly increased after treatment with morphine. Social behaviors not related to play, such as social exploration and crawling over/under were slightly decreased, while social grooming and non-social behavior were not affected by morphine treatment. Using sequential analysis, the dissociation between social behaviors related and unrelated to play was confirmed. Pinning and boxing/wrestling were highly significantly associated. In addition, crawling over/under significantly often preceded social grooming, and an association between social exploration and non-social behavior was found as well. Pinning and boxing/wrestling appeared to be negatively associated with non-social behaviors, social exploration and crawling over/under. A negative association between social grooming and social exploration was also found. Upon treatment with morphine, no major effects on the sequential structure of social behavior were observed: pinning and boxing/wrestling appeared more associated with following/chasing, and the negative association between pinning and boxing/wrestling on the one hand and social exploration on the other was enhanced. Thus, morphine slightly increased the coherence of social play behavior. It is concluded that morphine exerts its effects on social play behavior by increasing social play behavior as a whole rather than by changing its structure, suggesting a key role for opioid systems in the regulation of social play behavior.", "The therapeutic and stimulant properties of methylphenidate (MP), a drug commonly prescribed for the treatment of attention deficit hyperactivity disorder, have been attributed to increases in synaptic dopamine (DA) concentrations resulting from the blockade of DA transporters. In addition to obvious difficulties inherent in any interspecies comparison, interpretation of preclinical studies done with MP is further complicated by different routes of administration in animals (i.v. and i.p.) compared with humans (oral). In the present study we compared the effects of i.p. and intragastric (oral) MP both on rat nucleus accumbens DA assessed by in vivo microdialysis and on locomotor activity measured in a photocell apparatus. We also compared regional brain uptake and plasma levels of [(3)H]MP after administration of 5 mg/kg via both routes. Intraperitoneal MP (5 and 10 mg/kg) was approximately twice as potent as intragastric MP in terms of increasing extracellular DA levels and in stimulating locomotion. This was consistent with the higher brain uptake of [(3)H]MP when given i.p. rather than intragastrically. The dose of 2 mg/kg produced significant increases in both measurements when administered i.p., but not intragastrically. This study shows that relatively low doses of MP (2 mg i.p. and 5 mg intragastric) significantly increase extracellular DA and locomotor activity and indicates that the differences in the neurochemical and behavioral effects of MP between the intragastric and the i.p. routes are due to central drug bioavailability.", "Psychostimulants and behavior therapy have been postulated to be effective in treating attention-deficit hyperactivity disorder (ADHD) by compensating for a pathologically elevated reward threshold, but no studies have compared reinforcement to psychostimulants in maintaining task performance. The separate and combined effects of methylphenidate (MPH, 0.6 mg/kg) and a behavioral intervention (reward plus response cost) were assessed on a continuous performance test (CPT, a measure of sustained attention) modified to deliver auditory feedback contingent upon the subject's responses. Each of 22 children (6-10 years old) with ADHD were tested under four treatment conditions: placebo + feedback, placebo + behavioral contingencies, MPH + feedback, and MPH + contingencies. CPT performance, indexed by d' (ability to discriminate between target and false targets), was significantly better with MPH than with placebo, showing reduced deterioration over time. Contingency treatment improved mean d' compared to placebo + feedback but, in contrast, had no effect on the slope of performance deterioration. Addition of contingencies to MPH did not yield further improvement. The results indicate that MPH improved sustained attention on a laboratory task (and reduced task-irrelevant and other disinhibited behaviors), whereas behavioral contingencies did not. These findings suggest that, although both interventions improved stimulus discrimination processes, only MPH enhanced processes that mediate the regulation of effort over time. In addition, the disjunction between the effects of reward and of MPH provides evidence that psychostimulant effects on attention are only partially explained by the stimulation of brain centers associated with reward.", "Methamphetamine (MA) addiction is a growing epidemic worldwide. Chronic MA use has been shown to lead to neurotoxicity in rodents and humans. Magnetic resonance imaging (MRI) studies in MA users have shown enlarged striatal volumes and positron emission tomography (PET) studies have shown decreased brain glucose metabolism (BGluM) in the striatum of detoxified MA users. The present study examines structural changes of the brain, observes microglial activation, and assesses changes in brain function, in response to chronic MA treatment. Rats were randomly split into three distinct treatment groups and treated daily for four months, via i.p. injection, with saline (controls), or low dose (LD) MA (4 mg/kg), or high dose (HD) MA (8 mg/kg). Sixteen weeks into the treatment period, rats were injected with a glucose analog, [18F] fluorodeoxyglucose (FDG), and their brains were scanned with micro-PET to assess regional BGluM. At the end of MA treatment, magnetic resonance imaging at 21T was performed on perfused rats to determine regional brain volume and in vitro [3H]PK 11195 autoradiography was performed on fresh-frozen brain tissue to measure microglia activation. When compared with controls, chronic HD MA-treated rats had enlarged striatal volumes and increases in [3H]PK 11195 binding in striatum, the nucleus accumbens, frontal cortical areas, the rhinal cortices, and the cerebellar nuclei. FDG microPET imaging showed that LD MA-treated rats had higher BGluM in insular and somatosensory cortices, face sensory nucleus of the thalamus, and brainstem reticular formation, while HD MA-treated rats had higher BGluM in primary and higher order somatosensory and the retrosplenial cortices, compared with controls. HD and LD MA-treated rats had lower BGluM in the tail of the striatum, rhinal cortex, and subiculum and HD MA also had lower BGluM in hippocampus than controls. These results corroborate clinical findings and help further examine the mechanisms behind MA-induced neurotoxicity.", "The prescribed use of methylphenidate (Ritalin) in the treatment of attention deficit hyperactivity disorder has risen dramatically in recent years. The relative roles of dopamine, norepinephrine, and serotonin in the therapeutic action of these drugs was assessed by comparing the responses of extracellular nucleus accumbens dopamine and serotonin and hippocampus norepinephrine to the acute administration of low methylphenidate and amphetamine doses. The comparative neurochemical profiles in response to methylphenidate and amphetamine suggest that the norepinephrine effects may play an important role in the therapeutic effects of low doses of psychostimulants. In addition, to assess possible long-term consequences of prolonged exposure to this drug, we examined whether changes in the locomotor response occurred with repeated administration of these stimulant doses. Threshold doses of methylphenidate (0.5-1.0 mg/kg) or amphetamine (0.1-0.25 mg/kg) were administered twice daily, and then animals were tested in response to 2.5 mg/kg methylphenidate or 0.5 mg/kg amphetamine. Our results provide evidence that low-dose stimulant administration can result in the development of behavioral sensitization, which is evident in the subsequent behavioral response to the drug. The relevance of these data to the therapeutic uses of these drugs is discussed within the context of the many variables that can affect the behavioral and neurochemical responses to stimulants.", "The social play of pairs of juvenile rats can be brought under tight experimental control using social deprivation, and it can be objectively quantified by measurement of pinning behavior. Research and conceptual issues concerning this paired-encounter procedure are summarized, including issues related to measurement, gender differences (and the absence thereof), relations between play and aggression, the regulatory processes interacting with and underlying play, the neurochemical and neuroanatomical substrates of play, the functions of play in dominance and other adult behaviors. Existing results suggest the operation of a harmoniously operating brain process which generates a unique emotive brain process that is appropriately referred to as social play. Although the concept of play remains to be adequately defined, the position is advocated that rigorous psychobiological analysis will ultimately provide an empirical definition based upon neural circuit characteristics. Analysis of the underlying circuits may help reveal the manner in which more complex levels of behavioral competence arise ontogenically, and work in the area may yield clues to the genesis of several psychopathologies.", "Moderate doses of amphetamine and methylphenidate profoundly depress play fighting in juvenile rats. To test the idea that this behavioral effect was dependent on the release of catecholamines (CAs) we administered haloperidol (0.05-0.8 mg/kg), chlorpromazine (0.5-5 mg/kg), phenoxybenzamine (0.5-20 mg/kg) or propranolol (0.5-20 mg/kg) alone or in combination with 0.5 or 1 mg/kg d-amphetamine sulfate. None of these CA antagonists reversed the suppression of play fighting (indexed by pinning) caused by amphetamine, but at higher doses haloperidol, chlorpromazine and phenoxybenzamine depressed both pinning and rearing. The presynaptic NE agonist clonidine (0.05-0.2 mg/kg) also failed to block the effects of amphetamine on play; instead it too depressed both pinning and rearing. Finally the CA synthesis inhibitor, alpha-methyltyrosine (total dose: 100 mg/kg) did not attenuate the suppression of play by amphetamine. Ephedrine (10-80 mg/kg) mimicked the effects of amphetamine on pinning, but apomorphine did not. At doses from 0.125-0.5 mg/kg apomorphine stimulated pinning while 1 mg/kg had no effect. The present findings confirm earlier reports that amphetamine suppresses play fighting but the mechanism of action remains obscure.", "Catecholamine stimulant drugs are highly efficacious treatments for attention deficit/ hyperactivity disorders (AD/HD). Catecholamine modulation in humans influences performance of numerous cognitive tasks, including tests of attention and working memory (WM). Clear delineation of the effects of methylphenidate upon such cognitive functions in AD/HD would enhance understanding of the effects of drug treatment. Here we present a double-blind, placebo-controlled study of the cognitive effects of an acute dose of methylphenidate (c. .5 mg/kg) in 14 boys aged 10.86 (+/- 1.19) years meeting criteria for DSM-IV AD/HD. Current behaviour was ascertained using Conners' teacher and parent self-report questionnaires and IQ was tested using sub-tests from WISC-III-UK. Tests from the Cambridge Neuropsychological Test Automated Battery (CANTAB) were selected to assess visuo-spatial recognition memory, spatial WM, planning, visual-search and attentional-set shifting. Methylphenidate improved spatial WM, attentional-set shifting and visual-search task performance. Correlational analyses suggested possible relationships between WM capacity and spatial WM performance improvement. Also, poor performance on the attentional-set shifting task on placebo was associated with increased errors on the spatial WM task on placebo. Methylphenidate may selectively improve both underlying cognitive difficulties in tasks dependent on intact fronto-striatal structures, and clinical symptoms of AD/HD. Pre-treatment measures may have some predictive value in determining individual differences in drug response.", "Low doses of psychostimulants, such as methylphenidate (MPH), are widely used in the treatment of attention-deficit/hyperactivity disorder (ADHD). Surprisingly little is known about the neural mechanisms that underlie the behavioral/cognitive actions of these drugs. The prefrontal cortex (PFC) is implicated in ADHD. Moreover, dopamine (DA) and norepinephrine (NE) are important modulators of PFC-dependent cognition. To date, the actions of low-dose psychostimulants on PFC DA and NE neurotransmission are unknown. In vivo microdialysis was used to compare the effects of low-dose MPH on NE and DA efflux within the PFC and select subcortical fields in male rats. Doses used (oral, 2.0 mg/kg; intraperitoneal, .25-1.0 mg/kg) were first determined to produce clinically relevant plasma concentrations and to facilitate both PFC-dependent attention and working memory. At low doses that improve PFC-dependent cognitive function and that are devoid of locomotor-activating effects, MPH substantially increases NE and DA efflux within the PFC. In contrast, outside the PFC these doses of MPH have minimal impact on NE and DA efflux. The current observations suggest that the therapeutic actions of low-dose psychostimulants involve the preferential activation of catecholamine neurotransmission within the PFC." ]
Biomaterials as barriers or deterrents to prevent compression of neural structures by postsurgical fibrosis	Failed back surgery syndrome is a situation where there is failure after lumbar surgery aimed at correcting lumbar disease that is characterized by continuous back and/or leg pain. Epidural fibrosis and adhesions are among the major causes of failed back surgery syndrome. In recent years, several biomaterials have been applied as barriers or deterrents to prevent the compression of neural structures by postsurgical fibrosis.	[ "Clinical and experimental studies have highlighted the significance of inflammation in coordinating wound repair and regeneration. However, it remains challenging to control the inflammatory response and tolerance at systemic levels without causing toxicity to injured tissues. Mesenchymal stem cells (MSCs) possess potent immunomodulatory properties and facilitate tissue repair by releasing exosomes, which generate a suitable microenvironment for inflammatory resolution. Exosomes contain several effective bioactive molecules and act as a cell-cell communication vehicle to influence cellular activities in recipient cells. During this process, the horizontal transfer of exosomal microRNAs (miRNAs) to acceptor cells, where they regulate target gene expression, is of particular interest for understanding the basic biology of inflammation ablation, tissue homeostasis, and development of therapeutic approaches. In this review, we describe a signature of three specific miRNAs (miR-21, miR-146a, and miR-181) present in human umbilical cord MSC-derived exosomes (MSC-EXO) identified microarray chip analysis and focus on the inflammatory regulatory functions of these immune-related miRNAs. We also discuss the potential mechanisms contributing to the resolution of wound inflammation and tissue healing.", "Failed back surgery syndrome (FBSS) is a condition in which there is failure to improve satisfactorily after back surgery. It is characterized by intractable pain and various degrees of functional disability after lumbar spine surgery. It is estimated that this complication occurs in 5% to 10% of patients after spinal surgeries. The major causes of FBSS are fibrosis and adhesions, spinal instability, recurrent herniated disk, and inadequate decompression. The purpose of this study is to report on the postsurgical outcome after a redo spinal surgery. We prospectively studied 50 patients with FBSS. The underlying pathology was identified and all the patients were treated surgically. Redo surgery was targeted at correcting the underlying pathology: removal of recurrent or residual disk, release of adhesions with neural decompression, and fusion with or without instrumentation. The postsurgical outcome was studied using the Oswestry Disability Questionnaire (ODQ). The average preoperative ODQ mean score was 80.8; the average postoperative ODQ mean score was 36.6 at 1 month and 24.2 at 1 year. Best scores were obtained at 3 months of follow-up in most cases. Successful outcome (>50% pain relief) could be achieved in 92% of the patients at 1 year. The current study shows that successful management of patients with FBSS could be achieved with proper patient selection, correct preoperative diagnosis, and adequate surgical procedure targeting the underlying pathology.", "The purpose was to check the influence of enteric nutrition on BUN in very elderly patients. Clinical data on patients in whom enteral feeding was initiated after a period of poor oral intake are presented. Patients with evidence of volume depletion, signs of gastrointestinal bleeding or medicines that might increase BUN were excluded. We evaluated 5 patients (mean age 90.6 ± 3 years) who were admitted to geriatric department. Mean plasma creatinine concentration was 1.17 ± 0.34 mg/dl, but mean estimated glomerular filtration rate (eGFR) was 41.6 ± 17 ml/min/1.73 m(2). Enteral nutrition was administered at a dose of mean 1,580 ± 53ml/day at mean duration of 9 ± 4 days. Mean BUN was 52 ± 30 mg/dl at baseline, increases to 109 ± 9.4 mg/dl after initiation of feeding and decreased to 82 ± 1.1mg/dl with reduction of dose of enteral nutrition. Our conclusion was that initiation of enteral feeding may induce a large accumulation of nitrogen waste products in elderly patients in whom serum creatinine is an unreliable indicator of kidney function. High protein intake should be considered in differential diagnosis of disproportionate high increment of BUN.", "The therapeutic potential of mesenchymal stromal cells (MSCs) may be largely mediated by paracrine factors contained in microvesicles (MV) released from intracellular endosomes. A systematic review of controlled interventional animal studies was performed to identify models of organ injury where clinical translation of MSC-derived microvesicle therapy appears most promising as regenerative therapy. A total of 190 published articles were identified in our systematic search of electronic databases (MEDLINE, EMBASE, PUBMED). After screening for eligibility, a total of 17 controlled studies testing MSC-derived MVs as therapeutic interventions in animal models of disease underwent comprehensive review, quality assessment, and data extraction. Thirteen studies addressed the regenerative potential following organ injury. Six studies were included on acute kidney injury, 4 on myocardial infarction and reperfusion injury, 1 on hind limb ischemia, 1 on liver injury, and 1 on hypoxic lung injury. Four studies addressed immunological effects of MSC-derived MVs on inhibiting tumor growth. Twelve studies (71%) provided explicit information regarding the number of animals allocated to treatment or control groups. Five studies (29%) randomly assigned animals to treatment or control groups and only 1 study (6%) reported on blinding. Therapeutic intervention involved isolation of exosomes (40-100 nm) in eight studies, while nine studies tested unfractionated microvesicles (<1,000 nm). In studies of tissue regeneration, all 13 reported that treatment with MSC-derived MVs improved at least one major/clinical parameter associated with organ dysfunction. Three of 4 studies evaluating the inhibition of tumor growth reported benefit. In preclinical studies, the use of MSC-derived MVs is strongly associated with improved organ function following injury and may be useful for inhibiting tumor growth. Improved preclinical study quality in terms of treatment allocation reporting, randomization and blinding will accelerate needed progress towards clinical trials that should assess feasibility and safety of this therapeutic approach in humans.", "Mesenchymal stem cell (MSC)-derived exosomes have diverse functions in regulating wound healing and inflammation; however, the molecular mechanism of human umbilical cord MSC (hUCMSC)-derived exosomes in regulating burn-induced inflammation is not well understood. We found that burn injury significantly increased the inflammatory reaction of rats or macrophages exposed to lipopolysaccharide (LPS), increased tumor necrosis factor α (TNF-α) and interleukin-1β (IL-1β) levels and decreased IL-10 levels. hUCMSC-exosome administration successfully reversed this reaction. Further studies showed that miR-181c in the exosomes played a pivotal role in regulating inflammation. Compared to control hUCMSC-exosomes, hUCMSC-exosomes overexpressing miR-181c more effectively suppressed the TLR4 signaling pathway and alleviated inflammation in burned rats. Administration of miR-181c-expressing hUCMSC-exosomes or TLR4 knockdown significantly reduced LPS-induced TLR4 expression by macrophages and the inflammatory reaction. In summary, miR-181c expression in hUCMSC-exosomes reduces burn-induced inflammation by downregulating the TLR4 signaling pathway.", "The aim of this study was to evaluate the application and effects of a novel, nonswelling, polyethylene glycol-based hydrogel adhesion barrier and sealant in a canine laminectomy model of CSF leakage and adhesion formation. After full-width L-2 and L-5 laminectomies, 1-cm midline durotomies were created and sutured closed, except for the last 1-2 mm on the cranial end to create spontaneous CSF leakage. All 5 control animals received no further treatment. Experimental animals received hydrogel at both durotomy sites via either the Dual Liquid applicator (5 animals) or MicroMyst gas-assisted sprayer (5 animals). Sealing of the CSF leak was confirmed by Valsalva maneuver. At 2 months, 2 animals from each group were killed to evaluate dural healing and epidural adhesion formation. The remaining animals were similarly evaluated 4 months after surgery. One animal died at 66 days due to a cause unrelated to hydrogel treatment. In hydrogel-treated animals, all leaking durotomies were sealed intraoperatively. All animals recovered uneventfully. There were no treatment-related health effects. MicroMyst hydrogel application was more controlled, slower, and significantly less thick (p = 0.0094) than Dual Liquid application. All 5 control animals developed subcutaneous CSF accumulations under the incision within days of surgery, compared with only 1 of 10 hydrogel-treated animals (p = 0.002). At 2 and 4 months, control laminectomy sites showed extensive, dense epidural adhesions blending with neodura, compared with hydrogel-treated sites (p < 0.0001 and p = 0.0234, respectively). At 2 months in hydrogel-treated animals, gel filled the epidural space and no epidural adhesions were noted (p < 0.0001 relative to controls). At 4 months, the hydrogel was absorbed. The hydrogel space was filled with scant, loosely organized connective tissue. Hydrogel prevented CSF leakage and mitigated epidural scarring without affecting healing of the dura or laminectomy site. The safety profile of the hydrogel appears favorable due to its synthetic composition, polyethylene glycol chemistry, minimal local tissue response, and lack of neurological deficits. Controlled application of such hydrogel materials may reduce the incidence of postoperative leaks, prevent adhesion formation and thus improve recovery from spinal surgery, and improve identification of tissue planes for reoperations.", "Renal fibrosis is characterized by infiltration of interstitial inflammatory cells and release of inflammatory mediators, activation and proliferation of fibroblasts, and deposition of excessive extracellular matrix (ECM). The aim of this study was to evaluate the effect of human umbilical cord-derived mesenchymal stem cell (hucMSC) conditioned medium (CM) on renal tubulointerstitial inflammation and fibrosis. Renal interstitial fibrosis was prepared in vivo using the unilateral ureteral obstruction (UUO). Rats were divided randomly into Sham group, Sham group with CM, UUO group, and UUO group with CM. The effect of hucMSC-CM on kidney injury induced by UUO was assessed by detecting kidney histopathology, serum creatinine (SCr), and blood urea nitrogen (BUN). The levels of TNF-α, IL-6, and IL-1β in serum and kidney tissues were detected by ELISA. The expression of proteins associated with fibrosis and renal inflammation was investigated using immunohistochemical staining and western blotting. The effects of hucMSC-CM on the TGF-β1-induced epithelial-mesenchymal transition (EMT) process and on inflammation in NRK-52E cells were investigated by immunofluorescent staining, ELISA, and western blotting. hucMSC-CM reduced extracellular matrix deposition and inflammatory cell infiltration as well as release of inflammatory factors in UUO-induced renal fibrosis. Furthermore, hucMSC-CM markedly attenuated the EMT process and proinflammatory cytokines in rats with UUO and TGF-β1-induced NRK-52E cells. hucMSC-CM also inhibited the TLR4/NF-κB signaling pathway in vivo and in vitro. Our results suggest that hucMSC-CM has protective effects against UUO-induced renal fibrosis and that hucMSC-CM exhibits its anti-inflammatory effects through inhibiting TLR4/NF-κB signaling pathway activation.", "The RNA-Induced Silencing Complex (RISC) is a ribonucleoprotein particle composed of a single-stranded short interfering RNA (siRNA) and an endonucleolytically active Argonaute protein, capable of cleaving mRNAs complementary to the siRNA. The mechanism by which RISC cleaves a target RNA is well understood, however it remains enigmatic how RISC finds its target RNA. Here, we show, both in vitro and in vivo, that the accessibility of the target site correlates directly with the efficiency of cleavage, demonstrating that RISC is unable to unfold structured RNA. In the course of target recognition, RISC transiently contacts single-stranded RNA nonspecifically and promotes siRNA-target RNA annealing. Furthermore, the 5' part of the siRNA within RISC creates a thermodynamic threshold that determines the stable association of RISC and the target RNA. We therefore provide mechanistic insights by revealing features of RISC and target RNAs that are crucial to achieve efficiency and specificity in RNA interference.", "Epidural fibrosis is nonphysiological scar formation, usually at the site of neurosurgical access into the spinal canal, in the intimate vicinity of and around the origin of the radicular sheath. The formation of dense fibrous tissue causes lumbar and radicular pain. In addition to radicular symptoms, the formation of scar tissue may cause problems during reoperation. The authors aimed to investigate the effects of cross-linked high-molecular-weight hyaluronic acid (HA), an HA derivative known as HA gel, on the prevention of epidural fibrosis by using histopathological and biochemical parameters. Fifty-six adult female Sprague-Dawley rats were evaluated. The rats were divided into 4 groups. Rats in the sham group (n = 14) underwent laminectomy and discectomy and received no treatment; rats in the control group (n = 14) underwent laminectomy and discectomy and received 0.9% NaCl treatment in the surgical area; rats in the HA group (n = 14) received HA treatment at the surgical area after laminectomy and discectomy; and rats in the HA gel group (n = 14) underwent laminectomy and discectomy in addition to receiving treatment with cross-linked high-molecular-weight HA in the surgical area. All rats were decapitated after 4 weeks, and the specimens were evaluated histopathologically and biochemically. The results were statistically compared using the Mann-Whitney U-test. Compared with the sham and control groups, the HA and HA gel groups showed significantly lower fibroblast cell density and tissue hydroxyproline concentrations (p < 0.05). There was statistically significant lower dural adhesion and foreign-body reaction between the control and HA gel groups (p < 0.05). Granulation tissue and epidural fibrosis were significantly lower in the HA and HA gel groups compared with the sham group (p < 0.05). There were no significant differences in any histopathological parameters or biochemical values between Groups 3 and 4 (p > 0.05). Cross-linked high-molecular-weight HA had positive effects on the prevention of epidural fibrosis and the reduction of fibrotic tissue density. The efficacy of this agent should also be verified in further experimental and clinical studies.", "Sepsis causes over 200,000 deaths yearly in the US; better treatments are urgently needed. Administering bone marrow stromal cells (BMSCs -- also known as mesenchymal stem cells) to mice before or shortly after inducing sepsis by cecal ligation and puncture reduced mortality and improved organ function. The beneficial effect of BMSCs was eliminated by macrophage depletion or pretreatment with antibodies specific for interleukin-10 (IL-10) or IL-10 receptor. Monocytes and/or macrophages from septic lungs made more IL-10 when prepared from mice treated with BMSCs versus untreated mice. Lipopolysaccharide (LPS)-stimulated macrophages produced more IL-10 when cultured with BMSCs, but this effect was eliminated if the BMSCs lacked the genes encoding Toll-like receptor 4, myeloid differentiation primary response gene-88, tumor necrosis factor (TNF) receptor-1a or cyclooxygenase-2. Our results suggest that BMSCs (activated by LPS or TNF-alpha) reprogram macrophages by releasing prostaglandin E(2) that acts on the macrophages through the prostaglandin EP2 and EP4 receptors. Because BMSCs have been successfully given to humans and can easily be cultured and might be used without human leukocyte antigen matching, we suggest that cultured, banked human BMSCs may be effective in treating sepsis in high-risk patient groups." ]
M1/M2 classification of macrophages	Macrophages represent a heterogeneous cell population and are known to display a remarkable plasticity. In response to distinct micro-environmental stimuli, e.g., tumor stroma vs. infected tissue, they polarize into different cell subtypes. Originally, two subpopulations were defined: classically activated macrophages or M1, and alternatively activated macrophages or M2. Nowadays, the M1/M2 classification is considered as an oversimplified approach that does not adequately cover the total spectrum of macrophage phenotypes observed	[ "Macrophages display remarkable plasticity and can change their physiology in response to environmental cues. These changes can give rise to different populations of cells with distinct functions. In this Review we suggest a new grouping of macrophage populations based on three different homeostatic activities - host defence, wound healing and immune regulation. We propose that similarly to primary colours, these three basic macrophage populations can blend into various other 'shades' of activation. We characterize each population and provide examples of macrophages from specific disease states that have the characteristics of one or more of these populations.", "Recent studies have shown that macrophages play an important part in both tumor initiation and various key steps in growth and metastasis. These cells show a remarkable degree of plasticity during tumor development with a \"switch\" in macrophage phenotypes occurring during the course of tumor progression. During chronic inflammation they appear to predispose a given tissue to tumor initiation by the release of factors that promote neoplastic transformation. Following this, their phenotype shifts more toward one that is immunosuppressive and supports tumor growth, angiogenesis, and metastasis. In this review, we discuss the evidence for this plasticity of macrophage functions, the specific signaling mechanisms that may be regulating it, and the new targets for anticancer therapies highlighted by these findings.", "Atherosclerotic lesion-related thrombosis is the major cause of myocardial infarction and stroke, which together constitute the leading cause of mortality worldwide. The inflammatory response is considered as a predominant driving force in atherosclerotic plaque formation, growth and progression towards instability and rupture. Notably, accumulation of macrophages in the intima and emergence of a pro-inflammatory milieu are a characteristic feature of plaque progression, and these processes can be modulated by adaptive immune responses. Recently, novel evidences of onsite proliferation of macrophages in lesions and transdifferentiation of smooth muscle cells to macrophages have challenged the prevalent paradigm that macrophage accumulation mostly relies on recruitment of circulating monocytes to plaques. Furthermore, previously unrecognized roles of inflammatory cell subsets such as plasmacytoid dendritic cells, innate response activator B cells or CD8(+) T cells in atherosclerosis have emerged, as well as novel mechanisms by which regulatory T cells or natural killer T cells contribute to lesion formation. Here, we review and discuss these recent advances in our understanding of inflammatory processes in atherosclerosis.", "Metastasis proceeds through interaction between cancer cells and resident cells such as leukocytes and fibroblasts. An i.v. injection of a mouse renal cell carcinoma, Renca, into wild-type mice resulted in multiple metastasis foci in lungs and was associated with intratumoral accumulation of macrophages, granulocytes, and fibroblasts. A chemokine, CCL3, was detected in infiltrating cells and, to a lesser degree, tumor cells, together with an infiltration of leukocytes expressing CCR5, a specific receptor for CCL3. A deficiency of the CCL3 or CCR5 gene markedly reduced the number of metastasis foci in the lung, and the analysis using bone marrow chimeric mice revealed that both bone marrow- and non-bone marrow-derived cells contributed to metastasis formation. CCL3- and CCR5-deficient mice exhibited a reduction in intratumoral accumulation of macrophages, granulocytes, and fibroblasts. Moreover, intratumoral neovascularization, an indispensable process for metastasis, was attenuated in these gene-deficient mice. Intrapulmonary expression of matrix metalloproteinase (MMP)-9 and hepatocyte growth factor (HGF) was enhanced in wild-type mice, and the increases were markedly diminished in CCL3- and CCR5-deficient mice. Furthermore, MMP-9 protein was detected in macrophages and granulocytes, the cells that also express CCR5 and in vitro stimulation by CCL3-induced macrophages to express MMP-9. Intratumoral fibroblasts expressed CCR5 and HGF protein. In vitro CCL3 stimulated fibroblasts to express HGF. Collectively, the CCL3-CCR5 axis appears to regulate intratumoral trafficking of leukocytes and fibroblasts, as well as MMP-9 and HGF expression, and as a consequence to accelerate neovascularization and subsequent metastasis formation.", "CCR4 is recognized as a key receptor in Th2-associated immune processes, although very little is known about its role in innate immunity. Previous studies reported increased resistance to LPS-induced lethality in CCR4(-/-) mice compared with wild-type mice. This study demonstrates that CCR4(-/-) mice are similarly resistant to challenge with other TLR agonists, as well as bacterial peritonitis. Resistance was associated with enhanced early leukocyte recruitment, increased TLR expression, a skewed type 2 cytokine/chemokine profile, and improved bacterial clearance. Macrophages from CCR4(-/-) mice exhibited many features consistent with alternative activation, including elevated secretion of type 2 cytokines/chemokines and the found in inflammatory zone 1 (FIZZ1) protein. MyD88-dependent NF-kappaB signaling was significantly down-regulated in CCR4(-/-) macrophages, whereas p38 MAPK and JNK activation were conversely increased. These data stress the importance of CCR4 in macrophage differentiation and innate immune responses to pathogens, as well as the involvement of chemokine receptor expression in TLR signaling regulation.", "Inflammation is now a well-recognized hallmark of cancer progression. Tumor-associated macrophages (TAMs) are one of the major inflammatory cells that infiltrate murine and human tumors. While epidemiological studies indicate a clear correlation between TAM density and poor prognosis in a number of human cancers, transgenic studies and transcriptome profiling of TAMs in mice have established their crucial role in cancer progression. In fact, TAMs affect diverse aspects of cancer progression including tumor cell growth and survival, invasion, metastasis, angiogenesis, inflammation, and immunoregulation. New evidences have extended the repertoire of these cells to other tumor promoting activities like interactions with cancer stem cells, response to chemotherapy, and tumor relapse. These findings have triggered efforts to target TAMs and their associated molecules to modulate tumor progression. In particular, \"re-education\" to activate their anti-tumor potential or elimination of tumor promoting TAMs are strategies undergoing preclinical and clinical evaluation. Proof-of-principle studies indicate that TAM-centered therapeutic strategies may contribute to cancer therapy.", "Fibrosis is defined by the overgrowth, hardening, and/or scarring of various tissues and is attributed to excess deposition of extracellular matrix components including collagen. Fibrosis is the end result of chronic inflammatory reactions induced by a variety of stimuli including persistent infections, autoimmune reactions, allergic responses, chemical insults, radiation, and tissue injury. Although current treatments for fibrotic diseases such as idiopathic pulmonary fibrosis, liver cirrhosis, systemic sclerosis, progressive kidney disease, and cardiovascular fibrosis typically target the inflammatory response, there is accumulating evidence that the mechanisms driving fibrogenesis are distinct from those regulating inflammation. In fact, some studies have suggested that ongoing inflammation is needed to reverse established and progressive fibrosis. The key cellular mediator of fibrosis is the myofibroblast, which when activated serves as the primary collagen-producing cell. Myofibroblasts are generated from a variety of sources including resident mesenchymal cells, epithelial and endothelial cells in processes termed epithelial/endothelial-mesenchymal (EMT/EndMT) transition, as well as from circulating fibroblast-like cells called fibrocytes that are derived from bone-marrow stem cells. Myofibroblasts are activated by a variety of mechanisms, including paracrine signals derived from lymphocytes and macrophages, autocrine factors secreted by myofibroblasts, and pathogen-associated molecular patterns (PAMPS) produced by pathogenic organisms that interact with pattern recognition receptors (i.e. TLRs) on fibroblasts. Cytokines (IL-13, IL-21, TGF-beta1), chemokines (MCP-1, MIP-1beta), angiogenic factors (VEGF), growth factors (PDGF), peroxisome proliferator-activated receptors (PPARs), acute phase proteins (SAP), caspases, and components of the renin-angiotensin-aldosterone system (ANG II) have been identified as important regulators of fibrosis and are being investigated as potential targets of antifibrotic drugs. This review explores our current understanding of the cellular and molecular mechanisms of fibrogenesis.", "CC chemokine receptor (CCR)4, a high affinity receptor for the CC chemokines thymus and activation-regulated chemokine (TARC) and macrophage-derived chemokine (MDC), is expressed in the thymus and spleen, and also by peripheral blood T cells, macrophages, platelets, and basophils. Recent studies have shown that CCR4 is the major chemokine receptor expressed by T helper type 2 (Th2) polarized cells. To study the in vivo role of CCR4, we have generated CCR4-deficient (CCR4(-/-)) mice by gene targeting. CCR4(-/-) mice developed normally. Splenocytes and thymocytes isolated from the CCR4(-/-) mice failed to respond to the CCR4 ligands TARC and MDC, as expected, but also surprisingly did not undergo chemotaxis in vitro in response to macrophage inflammatory protein (MIP)-1alpha. The CCR4 deletion had no effect on Th2 differentiation in vitro or in a Th2-dependent model of allergic airway inflammation. However, CCR4(-/-) mice exhibited significantly decreased mortality on administration of high or low dose bacterial lipopolysaccharide (LPS) compared with CCR4(+/+) mice. After high dose LPS treatment, serum levels of tumor necrosis factor alpha, interleukin 1beta, and MIP-1alpha were reduced in CCR4(-/-) mice, and decreased expression of MDC and MIP-2 mRNA was detected in peritoneal exudate cells. Analysis of peritoneal lavage cells from CCR4(-/)- mice by flow cytometry also revealed a significant decrease in the F4/80(+) cell population. This may reflect a defect in the ability of the CCR4(-/-) macrophages to be retained in the peritoneal cavity. Taken together, our data reveal an unexpected role for CCR4 in the inflammatory response leading to LPS-induced lethality.", "Macrophages change their phenotype and biological functions depending on the microenvironment. In atherosclerosis, oxidative tissue damage accompanies chronic inflammation; however, macrophage phenotypic changes in response to oxidatively modified molecules are not known. To examine macrophage phenotypic changes in response to oxidized phospholipids that are present in atherosclerotic lesions. We show that oxidized phospholipid-treated murine macrophages develop into a novel phenotype (Mox) that is strikingly different from the conventional M1 and M2 macrophage phenotypes. Compared to M1 and M2, Mox macrophages show a different gene expression pattern, as well as decreased phagocytotic and chemotactic capacity. Treatment with oxidized phospholipids induces both M1 and M2 macrophages to switch to the Mox phenotype. Whole-genome expression array analysis and subsequent gene ontology clustering revealed that the Mox phenotype was characterized by abundant overrepresentation of Nrf2-mediated expression of redox-regulatory genes. In macrophages isolated from Nrf2(-/-) mice, oxidized phospholipid-induced gene expression and regulation of redox status were compromised. Moreover, we found that Mox macrophages comprise 30% of all macrophages in advanced atherosclerotic lesions of low-density lipoprotein receptor knockout (LDLR(-/-)) mice. Together, we identify Nrf2 as a key regulator in the formation of a novel macrophage phenotype (Mox) that develops in response to oxidative tissue damage. The unique biological properties of Mox macrophages suggest this phenotype may play an important role in atherosclerotic lesion development as well as in other settings of chronic inflammation.", "Nitric oxide (NO) and ornithine, products of NO synthase or arginase, respectively, have opposing biological activities. The effect of mediators of leukocyte activation and inhibition on arginine metabolism of resident mouse peritoneal exudate cells (MPEC) was determined. Factors that increased basal NO synthase activity, interferon (IFN)-gamma and lipopolysaccharide (LPS), decreased arginase activity in intact cells. Transforming growth factor (TGF)-beta1 decreased IFN-gamma-stimulated NO synthase activity and produced a reciprocal increase in urea and ornithine release. TGF-beta1 had no effect on the activity of these enzymes in LPS-stimulated MPEC. Corticosterone (Cort, 100 ng/ml) decreased the basal activity of both enzymes. However, Cort inhibited NO synthase activity and increased ornithine release in MPEC exposed to IFN-gamma or LPS. The difference between arginase activity in intact cells vs. that of cell lysates suggested intracellular inhibition of arginase activity. Products of NO synthase, NO and citrulline, were shown to inhibit MPEC arginase activity under maximal assay conditions. Intracellular pH was not altered by exposure of MPEC to LPS, IFN-gamma, TGF-beta, and Cort. This reciprocal change in arginine metabolism is proposed to be an important component of wound healing. Expression of NO synthase creates a cytotoxic environment that may be important to the early phase of wound healing. As wound healing progresses, increased arginase activity produces an environment favorable for fibroblast replication and collagen production." ]
Metabolic syndrome is a cluster of abnormalities that increases the risk for type 2 diabetes and atherosclerosis.	Metabolic syndrome is a cluster of abnormalities that increases the risk for type 2 diabetes and atherosclerosis. Plasma and serum water T	[ "Bone sialoprotein (BSP) and its messenger RNA were localized in developing human skeletal and nonskeletal tissues by means of immunohistochemistry and in situ hybridization. Both protein and mRNA were found in mature, bone-forming cells but not in their immature precursors. In addition, osteoclasts displayed positive immunostaining and high densities of autoradiographic grains by in situ hybridization experiments. BSP was expressed in fetal epiphyseal cartilage cells, particularly in hypertrophic chondrocytes of growth plates. Though neither the protein nor the mRNA were identified in a variety of other connective and nonconnective tissues, an unexpected finding was the expression of BSP in the trophoblast cells of placenta. These findings show that BSP is primarily an osteoblast-derived component of the bone matrix expressed at late stages of differentiation. We have also found that osteoclasts produce BSP, possibly as a mediator of cell attachment to bone.", "Although mast cell functions have classically been related to allergic responses, recent studies indicate that these cells contribute to other common diseases such as multiple sclerosis, rheumatoid arthritis, atherosclerosis, aortic aneurysm and cancer. This study presents evidence that mast cells also contribute to diet-induced obesity and diabetes. For example, white adipose tissue (WAT) from obese humans and mice contain more mast cells than WAT from their lean counterparts. Furthermore, in the context of mice on a Western diet, genetically induced deficiency of mast cells, or their pharmacological stabilization, reduces body weight gain and levels of inflammatory cytokines, chemokines and proteases in serum and WAT, in concert with improved glucose homeostasis and energy expenditure. Mechanistic studies reveal that mast cells contribute to WAT and muscle angiogenesis and associated cell apoptosis and cathepsin activity. Adoptive transfer experiments of cytokine-deficient mast cells show that these cells, by producing interleukin-6 (IL-6) and interferon-gamma (IFN-gamma), contribute to mouse adipose tissue cysteine protease cathepsin expression, apoptosis and angiogenesis, thereby promoting diet-induced obesity and glucose intolerance. Our results showing reduced obesity and diabetes in mice treated with clinically available mast cell-stabilizing agents suggest the potential of developing new therapies for these common human metabolic disorders.", "Glucokinase regulator (GCKR) encodes glucokinase regulatory protein (GKRP), a hepatocyte-specific inhibitor of the glucose-metabolizing enzyme glucokinase (GCK). Genome-wide association studies have identified a common coding variant within GCKR associated with multiple metabolic traits. This review focuses on recent insights into the critical role of GKRP in hepatic glucose metabolism that have stemmed from the study of human genetics. This knowledge has improved our understanding of glucose and lipid physiology and informed the development of targeted molecular therapeutics for diabetes. Rare GCKR variants have effects on GKRP expression, localization, and activity. These variants are collectively associated with hypertriglyceridaemia but are not causal. Crystal structures of GKRP and the GCK-GKRP complex have been solved, providing greater insight into the molecular interactions between these proteins. Finally, small molecules have been identified that directly bind GKRP and reduce blood glucose levels in rodent models of diabetes. GCKR variants across the allelic spectrum have effects on glucose and lipid homeostasis. Functional analysis has highlighted numerous molecular mechanisms for GKRP dysfunction. Hepatocyte-specific GCK activation via small molecule GKRP inhibition may be a new avenue for type 2 diabetes treatment, particularly considering evidence indicating GKRP loss-of-function alone does not cause hypertriglyceridaemia.", "Glucose homeostasis is a vital and complex process, and its disruption can cause hyperglycaemia and type II diabetes mellitus. Glucokinase (GK), a key enzyme that regulates glucose homeostasis, converts glucose to glucose-6-phosphate in pancreatic β-cells, liver hepatocytes, specific hypothalamic neurons, and gut enterocytes. In hepatocytes, GK regulates glucose uptake and glycogen synthesis, suppresses glucose production, and is subject to the endogenous inhibitor GK regulatory protein (GKRP). During fasting, GKRP binds, inactivates and sequesters GK in the nucleus, which removes GK from the gluconeogenic process and prevents a futile cycle of glucose phosphorylation. Compounds that directly hyperactivate GK (GK activators) lower blood glucose levels and are being evaluated clinically as potential therapeutics for the treatment of type II diabetes mellitus. However, initial reports indicate that an increased risk of hypoglycaemia is associated with some GK activators. To mitigate the risk of hypoglycaemia, we sought to increase GK activity by blocking GKRP. Here we describe the identification of two potent small-molecule GK-GKRP disruptors (AMG-1694 and AMG-3969) that normalized blood glucose levels in several rodent models of diabetes. These compounds potently reversed the inhibitory effect of GKRP on GK activity and promoted GK translocation both in vitro (isolated hepatocytes) and in vivo (liver). A co-crystal structure of full-length human GKRP in complex with AMG-1694 revealed a previously unknown binding pocket in GKRP distinct from that of the phosphofructose-binding site. Furthermore, with AMG-1694 and AMG-3969 (but not GK activators), blood glucose lowering was restricted to diabetic and not normoglycaemic animals. These findings exploit a new cellular mechanism for lowering blood glucose levels with reduced potential for hypoglycaemic risk in patients with type II diabetes mellitus.", "The adipocyte-derived secretory protein adiponectin has been widely studied and shown to have potent insulin-sensitizing, antiapoptotic, and anti-inflammatory properties. While its biosynthesis is well understood, its fate, once in circulation, is less well established. Here, we examine the half-life of adiponectin in circulation by tracking fluorescently labeled recombinant adiponectin in the circulation, following it to its final destination in the hepatocyte. Despite its abundant presence in plasma, adiponectin is cleared rapidly with a half-life of approximately 75 min. A more bioactive version carrying a mutation at cysteine 39 is cleared within minutes. Even though steady-state levels of adiponectin differ between male and female mice, we failed to detect any differences in clearance rates, suggesting that differences in plasma are mostly due to differential production rates. In a metabolically challenged state (high-fat diet exposure or in an ob/ob background), adiponectin levels are reduced in plasma and clearance is significantly prolonged, reflecting a dramatic drop in adiponectin production levels. Combined, these results show a surprisingly rapid turnover of adiponectin with multiple fat pads contributing to the plasma levels of adiponectin and clearance mediated primarily by the liver. It is surprising that despite high-level production and rapid clearance, plasma levels of adiponectin remain remarkably constant.", "Fibrosis is increasingly appreciated as a major player in adipose tissue dysfunction. In rapidly expanding adipose tissue, pervasive hypoxia leads to an induction of HIF1α that in turn leads to a potent profibrotic transcriptional program. The pathophysiological impact of adipose tissue fibrosis is likely to play an equally important role on systemic metabolic alterations as fibrotic conditions play in the liver, heart, and kidney. Here, we discuss recent advances in our understanding of the genesis, modulation, and systemic impact of excessive extracellular matrix (ECM) accumulation in adipose tissue of both rodents and humans and the ensuing impact on metabolic dysfunction.", "Metastasis follows the inappropriate activation of a genetic programme termed invasive growth, which is a physiological process that occurs during embryonic development and post-natal organ regeneration. Burgeoning evidence indicates that invasive growth is also executed by stem and progenitor cells, and is usurped by cancer stem cells. The MET proto-oncogene, which is expressed in both stem and cancer cells, is a key regulator of invasive growth. Recent findings indicate that the MET tyrosine-kinase receptor is a sensor of adverse microenvironmental conditions (such as hypoxia) and drives cell invasion and metastasis through the transcriptional activation of a set of genes that control blood coagulation." ]
Integrin Receptors in Cancer Therapy	Angiogenesis, sprouting of new blood vessels from pre-existing vasculatures, plays a critical role in regulating tumor growth. Binding interactions between integrin, a heterodimeric transmembrane glycoprotein receptor, and its extracellular matrix (ECM) protein ligands govern the angiogenic potential of tumor endothelial cells. Integrin receptors are attractive targets in cancer therapy due to their overexpression on tumor endothelial cells, but not on quiescent blood vessels. These receptors are finding increasing applications in anti-angiogenic therapy via targeted delivery of chemotherapeutic drugs and nucleic acids to tumor vasculatures. The current article attempts to provide a retrospective account of the past developments, highlight important contemporary contributions and unresolved set-backs of this emerging field.	[ "Tumor angiogenesis appears to be achieved by the expression of vascular endothelial growth factor (VEGF) within solid tumors that stimulate host vascular endothelial cell mitogenesis and possibly chemotaxis. VEGF's angiogenic actions are mediated through its high-affinity binding to 2 endothelium-specific receptor tyrosine kinase, Flt-1 (VEGFR1), and Flk-1/KDR (VEGFR2). RNA interference-mediated knockdown of protein expression at the messenger RNA level provides a new therapeutic strategy to overcome various diseases. To achieve high efficacy in RNA interference-mediated therapy, it is critical to develop an efficient delivering system to deliver small interference RNA (siRNA) into tissues or cells site-specifically. We previously reported an angiogenic endothelial cell-targeted polymeric gene carrier, PEI-g-PEG-RGD. This targeted carrier was developed by the conjugation of the ανβ3/ανβ5 integrin-binding RGD peptide (ACDCRGDCFC) to the cationic polymer, branched polyethylenimine, with a hydrophilic polyethylene glycol (PEG) spacer. In this study, we used PEI-g-PEG-RGD to deliver siRNA against VEGFR1 into tumor site. The physicochemical properties of PEI-g-PEG-RGD/siRNA complexes was evaluated. Further, tumor growth profile was also investigated after systemic administration of PEI-g-PEG-RGD/siRNA complexes.", "Despite the impressive results obtained in animal models, the clinical use of tumor necrosis factor-alpha (TNF) as an anticancer drug is limited by severe toxicity. We have shown previously that targeted delivery of TNF to aminopeptidase N (CD13), a marker of angiogenic vessels, improved the therapeutic index of this cytokine in tumor-bearing mice. To assess whether the vascular-targeting approach could be extended to other markers of tumor blood vessels, in this work, we have fused TNF with the ACDCRGDCFCG peptide, a ligand of alpha(V) integrins by recombinant DNA technology. We have found that subnanogram doses of this conjugate are sufficient to induce antitumor effects in tumor-bearing mice when combined with melphalan, a chemotherapeutic drug. Cell adhesion assays and competitive binding experiments with anti-integrin antibodies showed that the Arg-Gly-Asp moiety interacts with cell adhesion receptors, including alpha(V)beta(3) integrin, as originally postulated. In addition, ACGDRGDCFCG-mouse TNF conjugate induced cytotoxic effects in standard cytolytic assays, implying that ACGDRGDCFCG-mouse TNF conjugate can also bind TNF receptors and trigger death signals. These results indicate that coupling TNF with alpha(V) integrin ligands improves its antineoplastic activity and supports the concept that vascular targeting is a strategy potentially applicable to different endothelial markers, not limited to CD13.", "In this work, peptides designed to selectively interact with cellular receptors involved in the regulation of angiogenesis were anchored to oligo-ethylene glycol-capped gold nanoparticles (AuNPs) and used to evaluate the modulation of vascular development using an ex ovo chick chorioallantoic membrane assay. These nanoparticles alter the balance between naturally secreted pro- and antiangiogenic factors, under various biological conditions, without causing toxicity. Exposure of chorioallantoic membranes to AuNP-peptide activators of angiogenesis accelerated the formation of new arterioles when compared to scrambled peptide-coated nanoparticles. On the other hand, antiangiogenic AuNP-peptide conjugates were able to selectively inhibit angiogenesis in vivo. We demonstrated that AuNP vectorization is crucial for enhancing the effect of active peptides. Our data showed for the first time the effective control of activation or inhibition of blood vessel formation in chick embryo via AuNP-based formulations suitable for the selective modulation of angiogenesis, which is of paramount importance in applications where promotion of vascular growth is desirable (eg, wound healing) or ought to be contravened, as in cancer development.", "In vivo selection of phage display libraries have been exploited successfully in the past to isolate various high affinity conformationally strained cyclic peptide ligands (CX(5-7)C, peptides flanked by a cysteine residue on each side) for integrin receptors capable of selectively homing to tumor vasculatures. Previously, such phase display library studies have shown that integrin alpha 5 beta 1 binds with high affinity to cyclic peptides containing CRGDGWC motif. Herein we show that a lipopeptide with just the RGDGW motif (without the flanking cysteine groups) covalently attached to the lysine residue of a monolysinylated cationic amphiphile (RGDGWK-lipopeptide 1) delivers genes to cultured cells preferably via alpha 5 beta 1 integrins. Importantly, remarkable tumor growth inhibition was observed when the electrostatic complex of the RGDGWK-lipopeptide 1 and the anti-cancer p53 gene was intravenously administered in C57BL/6J mice bearing the aggressive B16F10 tumor. Immunohistochemical staining of mice tumor cryosections with vasculature markers combined with monitoring expression of the green fluorescence protein in the same tumor cryosections revealed that the RGDGWK-lipopeptide 1 targets genes to tumor vasculatures. The colocalization of the TUNEL (terminal deoxyuridine triphosphate nick-end labeling, a widely used marker of apoptosis) and VE-cadherin (markers of tumor endothelial cells) positive cells in tumor cryosections support the notion that the remarkable tumor growth inhibition property of the RGDGWK-lipopeptide 1:p53 complex is initiated through apoptosis of the tumor endothelial cells.", "Efficient and site-specific delivery of therapeutic drugs is a critical challenge in clinical treatment of cancer. Nano-sized carriers such as liposomes, micelles, and polymeric nanoparticles have been investigated for improving bioavailability and pharmacokinetic properties of therapeutics via various mechanisms, for example, the enhanced permeability and retention (EPR) effect. Further improvement can potentially be achieved by conjugation of targeting ligands onto nanocarriers to achieve selective delivery to the tumour cell or the tumour vasculature. Indeed, receptor-targeted nanocarrier delivery has been shown to improve therapeutic responses both in vitro and in vivo. A variety of ligands have been investigated including folate, transferrin, antibodies, peptides and aptamers. Multiple functionalities can be incorporated into the design of nanoparticles, e.g., to enable imaging and triggered intracellular drug release. In this review, we mainly focus on recent advances on the development of targeted nanocarriers and will introduce novel concepts such as multi-targeting and multi-functional nanoparticles.", "We engineered a fusion protein, mrIL-12vp [mouse recombinant interleukin (IL)-12 linked to vascular peptide], linking the vascular homing peptide CDCRGDCFC (RGD-4C), a ligand for alphavbeta3 integrin, to mrIL-12 to target IL-12 directly to tumor neovasculature. The fusion protein stimulated IFN-gamma production in vitro and in vivo, indicating its biological activity was consistent with mrIL-12. Immunofluorescence techniques showed mrIL-12vp specifically bound to alphavbeta3 integrin-positive cells but not to alphavbeta3 integrin-negative cells. In corneal angiogenesis assays using BALB/c mice treated with either 0.5 microg/mouse/d of mrIL-12vp or mrIL-12 delivered by subcutaneous continuous infusion, mrIL-12vp inhibited corneal neovascularization by 67% compared with only a slight reduction (13%) in angiogenesis in the mrIL-12-treated animals (P = 0.008). IL-12 receptor knockout mice given mrIL-12vp showed a marked decrease in the area of corneal neovascularization compared with mice treated with mrIL-12. These results indicate that mrIL-12vp inhibits angiogenesis through IL-12-dependent and IL-12-independent mechanisms, and its augmented antiangiogenic activity may be due to suppression of endothelial cell signaling pathways by the RGD-4C portion of the fusion protein. Mice injected with NXS2 neuroblastoma cells and treated with mrIL-12vp showed significant suppression of tumor growth compared with mice treated with mrIL-12 (P = 0.03). Mice did not show signs of IL-12 toxicity when treated with mrIL-12vp, although hepatic necrosis was present in mrIL-12-treated mice. Localization of IL-12 to neovasculature significantly enhances the antiangiogenic effect, augments antitumor activity, and decreases toxicity of IL-12, offering a promising strategy for expanding development of IL-12 for treatment of cancer patients.", "Targeted delivery of therapeutics to tumor neovasculature is potentially a powerful approach for selective cancer treatment. Integrins are heterodimeric transmembrane proteins involved in cell adhesion and cell signaling, and their expression is commonly upregulated in cancers and inflammatory diseases. The α(v)β(3) integrin is differentially upregulated on angiogenic endothelial cells as well as on many cancer cells. Here we demonstrate the differential targeting of cisplatin prodrug-encapsulated poly(d,l-lactic-co-glycolic acid)-block-polyethylene glycol (PLGA-PEG) nanoparticles (NPs) to the α(v)β(3) integrin on cancer cells using the cyclic pentapeptide c(RGDfK). Cisplatin is one of the most widely used anticancer drugs, and approaches that can improve its therapeutic index are of broad importance. The RGD-targeted Pt(IV)-encapsulated NPs displayed enhanced cytotoxicity as compared to cisplatin administered in its conventional dosage form in model prostate and breast cancer epithelial cells in vitro. Cytotoxicities were also elevated in comparison to those of previously reported systems, a small molecule Pt(IV)-RGD conjugate and a Pt(IV) nanoscale coordination polymer carrying RGD moieties. This result encouraged us also to evaluate the anticancer effect of the new construct in an animal model. The RGD-targeted PLGA-PEG NPs were more efficacious and better tolerated by comparison to cisplatin in an orthotopic human breast cancer xenograft model in vivo.", "Isoliquiritigenin (ISL), a natural anti-breast cancer dietary compound, has poor delivery characteristics and low bioavailability. In order to promote the therapeutic outcome of ISL, a tumor-targeting lipid-polymer hybrid nanoparticle (NP) system modified by tumor-homing iRGD peptides has been developed. The hybrid NPs were prepared by a modified single-step nanoprecipitation method to encapsulate ISL. iRGD peptides were anchored on the surface by a postinsertion method (ISL-iRGD NPs). The stable lipid-polymer structure of ISL-iRGD NPs, with high encapsulation and loading efficiency, was confirmed. Compared to free ISL and non-iRGD-modified counterparts, ISL-iRGD NPs showed higher cytotoxicity and cell apoptosis against the different type of breast cancer cells. This was attributable to higher cellular accumulation mediated by the iRGD-integrin recognition and the nanoscale effect. More importantly, based on the active tumor-tissue accumulation by iRGD peptides and the prolonged in vivo circulation by the stealth nanostructure, ISL-iRGD NPs displayed higher tumor-growth inhibition efficiency in 4T1-bearing breast-tumor mouse models. Therefore, the constructed iRGD modified lipid-polymer hybrid NPs would provide a promising drug-delivery strategy to improve ISL in anti-breast cancer efficacy.", "Tumor targeting drug delivery systems are being the ideal carriers of systemic administration for tumor therapy. We have reported previously that RGD peptide (arginine-glycine-aspartic acid)-modified liposomes containing drugs could increase targeting to tumor by binding with the integrin receptors overexpressed on tumor cells. RNA interference plays an important role on down-regulation of P-glycoprotein (P-gp), which is a drug efflux transporter overexpressed on multi-drug-resistant (MDR) tumor cells. To improve MDR tumor therapy, sequential treatment strategy with RGD-modified liposomes containing P-gp targeted small interference (siRNA) or doxorubicin (DOX) was reported in this study. When targeted via RGD to tumor-cell-surface and tumor neovasculature endothelial cell receptors, cationic liposomes could specifically deliver siRNAs to tumor cells and thus reverse drug resistance by down-regulation of P-gp, following administration of targeted liposomes containing DOX that inhibit formerly drug-resistant tumors. From the current results, the combination use of DOX and P-gp targeted siRNA showed significantly higher in vitro cytotoxicity in tumor cells than liposomal DOX alone. In vivo studies in a mouse model of drug-resistant MCF7/A tumor demonstrated significantly greater inhibition of tumor growth followed by the sequential treatment of RGD-modified liposomes containing siRNA or DOX when compared to liposomal DOX alone. Also, ex vivo tissue imaging studies have shown the accumulation of siRNA and DOX in tumors at same site-specific manner. These results suggested that the sequential treatment of P-gp gene silencing and cytotoxic drug with RGD-modified liposome drug delivery system could be a promising clinical treatment for drug-resistant tumors.", "In this article, the American Cancer Society provides an overview of female breast cancer statistics in the United States, including data on incidence, mortality, survival, and screening. Approximately 231,840 new cases of invasive breast cancer and 40,290 breast cancer deaths are expected to occur among US women in 2015. Breast cancer incidence rates increased among non-Hispanic black (black) and Asian/Pacific Islander women and were stable among non-Hispanic white (white), Hispanic, and American Indian/Alaska Native women from 2008 to 2012. Although white women have historically had higher incidence rates than black women, in 2012, the rates converged. Notably, during 2008 through 2012, incidence rates were significantly higher in black women compared with white women in 7 states, primarily located in the South. From 1989 to 2012, breast cancer death rates decreased by 36%, which translates to 249,000 breast cancer deaths averted in the United States over this period. This decrease in death rates was evident in all racial/ethnic groups except American Indians/Alaska Natives. However, the mortality disparity between black and white women nationwide has continued to widen; and, by 2012, death rates were 42% higher in black women than in white women. During 2003 through 2012, breast cancer death rates declined for white women in all 50 states; but, for black women, declines occurred in 27 of 30 states that had sufficient data to analyze trends. In 3 states (Mississippi, Oklahoma, and Wisconsin), breast cancer death rates in black women were stable during 2003 through 2012. Widening racial disparities in breast cancer mortality are likely to continue, at least in the short term, in view of the increasing trends in breast cancer incidence rates in black women." ]
Critical Illnesses in Pregnant Women	Pregnancy is a normal physiologic process with the potential for pathologic states. Pregnancy has several unique characteristics including an utero-placental interface, a physiologic stress that can cause pathologic states to develop, and a maternal-foetal interface that can affect two lives simultaneously or in isolation. Critical illness in pregnant women may result from deteriorating preexisting conditions, diseases that are co-incidental to pregnancy, or pregnancy-specific conditions. Successful maternal and neonatal outcomes for parturients admitted to a maternal critical care facility are largely dependent on a multidisciplinary input to medical or surgical condition from critical care physicians, obstetric anaesthesiologists, obstetricians, obstetric physicians, foetal medicine specialists, neonatologists, and concerned specialists. Pregnant women requiring maternal critical care unit admission are relatively low in developed nations and range from 0.9% to 1%; but in our country, the admission rates of critically ill parturients range from 3% to 8%. Two-thirds of pregnant women requiring critical care are often unanticipated at the time of conception. In this review, we will look at critical illnesses in pregnant women with a specific focus on pregnancy-induced illnesses.	[ "The cardiopulmonary resuscitation guideline of Basic Cardiopulmonary Life Support (BCLS) for management of adult victims with cardiopulmonary arrest outside the hospital provides an algorithmic stepwise approach for optimal outcome of the victims by trained medics and paramedics. This guideline has been developed considering the need to have a universally acceptable practice guideline for India and keeping in mind the infrastructural limitations of some areas of the country. This guideline is based on evidence elicited in the international and national literature. In the absence of data from Indian population, the excerpts have been taken from international data, discussed with Indian experts and thereafter modified to make them practically applicable across India. The optimal outcome for a victim with cardiopulmonary arrest would depend on core links of early recognition and activation; early high-quality cardiopulmonary resuscitation, early defibrillation and early transfer to medical facility. These links are elaborated in a stepwise manner in the BCLS algorithm. The BCLS also emphasise on quality check for various steps of resuscitation.", "The various physiological changes in pregnancy make the parturient vulnerable for early and rapid desaturation. Severe hypoxaemia during intubation can potentially compromise two lives (mother and foetus). Thus tracheal intubation in the pregnant patient poses unique challenges, and necessitates meticulous planning, ready availability of equipment and expertise to ensure maternal and foetal safety. The All India Difficult Airway Association (AIDAA) proposes a stepwise plan for the safe management of the airway in obstetric patients. These guidelines have been developed based on available evidence; wherever robust evidence was lacking, recommendations were arrived at by consensus opinion of airway experts, incorporating the responses to a questionnaire sent to members of the AIDAA and the Indian Society of Anaesthesiologists (ISA). Modified rapid sequence induction using gentle intermittent positive pressure ventilation with pressure limited to ≤20 cm H2O is acceptable. Partial or complete release of cricoid pressure is recommended when face mask ventilation, placement of supraglottic airway device (SAD) or tracheal intubation prove difficult. One should call for early expert assistance. Maternal SpO2 should be maintained ≥95%. Apnoeic oxygenation with nasal insufflation of 15 L/min oxygen during apnoea should be performed in all patients. If tracheal intubation fails, a second- generation SAD should be inserted. The decision to continue anaesthesia and surgery via the SAD, or perform fibreoptic-guided intubation via the SAD or wake up the patient depends on the urgency of surgery, foeto-maternal status and availability of resources and expertise. Emergency cricothyroidotomy must be performed if complete ventilation failure occurs.", "Outcomes from out-of-hospital cardiac arrest (OHCA) may improve if rescuers perform chest compressions (CCs) deeper than the previous recommendation of 38-51mm and consistent with the 2010 AHA Guideline recommendation of at least 51mm. The aim of this study was to assess the relationship between CC depth and OHCA survival. Prospective analysis of CC depth and outcomes in consecutive adult OHCA of presumed cardiac etiology from two EMS agencies participating in comprehensive CPR quality improvement initiatives. Multivariable logistic regression to calculate adjusted odds ratios (aORs) for survival to hospital discharge and favorable functional outcome. Among 593 OHCAs, 136 patients (22.9%) achieved return of spontaneous circulation, 63 patients (10.6%) survived and 50 had favorable functional outcome (8.4%). Mean CC depth was 49.8±11.0mm and mean CC rate was 113.9±18.1CCmin(-1). Mean depth was significantly deeper in survivors (53.6mm, 95% CI: 50.5-56.7) than non-survivors (48.8mm, 95% CI: 47.6-50.0). Each 5mm increase in mean CC depth significantly increased the odds of survival and survival with favorable functional outcome: aORs were 1.29 (95% CI 1.00-1.65) and 1.30 (95% CI 1.00-1.70) respectively. Deeper chest compressions were associated with improved survival and functional outcome following OHCA. Our results suggest that adhering to the 2010 AHA Guideline-recommended depth of at least 51mm could improve outcomes for victims of OHCA." ]
Proton-pump inhibitor use and bone fracture incidence and bone mineral density: a meta-analysis	This study's objective was to evaluate the association between proton-pump inhibitor (PPI) use and bone fracture incidence and bone mineral density (BMD) by meta-analyzing the estimates reported by epidemiological and cohort studies.	[ "Proton pump inhibitors (PPIs) are highly effective in the treatment of upper gastrointestinal acid-related conditions and are fast becoming one of the most frequently prescribed treatments in adult or older persons. Recent data show that long-term use of PPIs in older subjects is associated with important undesirable effects, including a higher risk of osteoporotic fractures. The mechanisms of this association are unclear and the relationship between the use of PPIs and parameters of bone mass and geometry has never been fully explored. This study investigates the relationship between the chronic use of PPIs and the parameters of bone mass (cortical and trabecular bone mineral density - vBMDc and vBMDt) and bone geometry (cortical and trabecular cross sectional area - tCSA and cCSA) in older individuals. The study population consisted of 1038 subjects (452 men and 586 women) 65years or older, selected from the InCHIANTI study, with complete information on computerized tomography performed at tibial level (pQCT) and on medications. Participants were classified as PPI users and nonusers based on self-report of PPI use over the last 15days, with PPI users (36 subjects, 14 men and 22 women) making up 3.4% of the study population (mean age 75.7±7.4years). The relationship between use of PPIs and pQCT bone parameters was tested by multivariate linear regression analysis adjusted for age, sex and several clinical factors and/or statistically confounding variables identified by partial correlation coefficient and Spearman partial rank order correlation coefficients, as appropriate (age, sex, BMI, caloric intake, IGF-1, IL-6, calcium, estradiol, bioavailable testosterone, vitamin D, parathyroid hormone, cross-sectional muscle area, and level of physical activity). PPI users showed age- and sex-adjusted lower vBMDt than nonusers (180.5±54.8 vs. 207.9±59.4, p=0.001). The inverse association between PPI use and vBMDt remained almost unchanged after adjustment for multiple confounders. There was no statistically significant difference in vBMDc, tCSA and cCSA between PPI users and nonusers. In community dwelling older persons, the use of PPIs is inversely associated with vBMDt, an early marker of the osteoporotic process. These findings suggest that PPI use might increase the risk of fractures in older subjects through its detrimental effects on trabecular bone.", "Previous studies evaluated the association between proton pump inhibitor (PPI) use and subsequent fracture risk, but they showed ambiguous results. Therefore, the objective was to evaluate this association in a different study population. Our findings show that there is probably no causal relationship between PPI use and hip fracture risk. Previous studies evaluated the association between PPI use and subsequent fracture risk, but they showed ambiguous results. To further test these conflicting results, the objective of this study was to evaluate the association between the use of PPIs and the risk of hip/femur fracture in a different study population. A case-control study was conducted using data from the Dutch PHARMO record linkage system. The study population included 6,763 cases aged 18 years and older with a first hip/femur fracture during enrollment and 26,341 age-, gender- and region-matched controls. Current users of PPIs had an increased risk of hip/femur fracture yielding an adjusted odds ratio (AOR) of 1.20 (95% CI 1.04-1.40). Fracture risk attenuated with increasing durations of use, resulting in AORs of 1.26 (95% CI 0.94-1.68) in the first 3 months, 1.31 (95% CI 0.97-1.75) between 3 and 12 months, 1.18 (95% CI 0.92-1.52) between 13 and 36 months and 1.09 (95% CI 0.81-1.47) for use longer than 36 months. Our findings show that there is probably no causal relationship between PPI use and hip fracture risk. The observed association may be the result of unmeasured distortions: although current use of PPIs was associated with a 1.2-fold increased risk of hip/femur fracture, the positive association was attenuated with longer durations of continuous use. Our findings do not support that discontinuation of PPIs decreases risk of hip fracture in elderly patients.", "Proton pump inhibitors (PPIs) are among the most widely used drugs worldwide. They are used to treat a number of gastroesophageal disorders and are usually prescribed as a long-term medication or even taken without a prescription. There are a number of clinical studies that associate PPI use with an increased cardiovascular risk. In this article, we review the clinical evidence for adverse cardiovascular effects of PPIs, and we discuss possible biological mechanisms by which PPIs can impair cardiovascular health.", "To determine whether there is an increased risk of hip fracture associated with the use of proton pump inhibitors in a Mediterranean area after adjusting for other potential risk factors. Retrospective multicenter case-control study carried out in 6 primary health care centers in Catalonia, Spain. Cases were patients aged 50years and over with a fragility hip fracture registered between January 2007 and December 2010, matched with 2 controls by sex and age. use of proton pump inhibitors (type, dosage) in the 5years previous to the hip fracture, socio-demographic data, body mass index, alcohol and tobacco consumption as well as health conditions and drugs associated with an increase risk of fragility hip fracture. 358 cases were matched with 698 controls. The mean age was 82years old in both groups. Women represented 77.1% in the case group and 76.9% in the control group. Crude association between proton pump inhibitors and hip fracture was 1.44 (95% CI, 1.09-1.89) and adjusted OR was 1.24 (95% CI, 0.93-1.65). No association was found with the continuous or discontinuous use of proton pump inhibitors, OR 1.17 (95% CI, 0.77-1.79), and OR of 1.16 (95% CI, 0.85-1.60) respectively. No association was found when restricting the analysis by sex, OR of 1.19 (95% CI, 0.27-5.14) or by age, younger or older than 80years, OR of 0.72 (95% CI, 0.24-2.15). The use of proton pump inhibitors was not associated with an increased risk of hip fracture after adjusting for other risk factors in a Mediterranean area. This result suggests the existence of protective environmental factors linked to this southern area of Europe that eventually could compensate for the potential harm produced by proton pump inhibitors.", "Defective absorption of calcium has been thought to exist in patients with achlorhydria. I compared absorption of calcium in its carbonate form with that in a pH-adjusted citrate form in a group of 11 fasting patients with achlorhydria and in 9 fasting normal subjects. Fractional calcium absorption was measured by a modified double-isotope procedure with 0.25 g of calcium used as the carrier. Mean calcium absorption (+/- S.D.) in the patients with achlorhydria was 0.452 +/- 0.125 for citrate and 0.042 +/- 0.021 for carbonate (P less than 0.0001). Fractional calcium absorption in the normal subjects was 0.243 +/- 0.049 for citrate and 0.225 +/- 0.108 for carbonate (not significant). Absorption of calcium from carbonate in patients with achlorhydria was significantly lower than in the normal subjects and was lower than absorption from citrate in either group; absorption from citrate in those with achlorhydria was significantly higher than in the normal subjects, as well as higher than absorption from carbonate in either group. Administration of calcium carbonate as part of a normal breakfast resulted in completely normal absorption in the achlorhydric subjects. These results indicate that calcium absorption from carbonate is impaired in achlorhydria under fasting conditions. Since achlorhydria is common in older persons, calcium carbonate may not be the ideal dietary supplement.", "Proton pump inhibitor (PPI) medications have been inconsistently shown to be associated with osteoporotic fractures. We examined the association of PPI use with bone outcomes (fracture, bone mineral density [BMD]). This prospective analysis included 161 806 postmenopausal women 50 to 79 years old, without history of hip fracture, enrolled in the Women's Health Initiative (WHI) Observational Study and Clinical Trials with a mean (SD) follow-up of 7.8 (1.6) years. Analyses were conducted for 130 487 women with complete information. Medication information was taken directly from drug containers during in-person interviews (baseline, year 3). The main outcome measures were self-reported fractures (hip [adjudicated], clinical spine, forearm or wrist, and total fractures) and for a subsample (3 densitometry sites), 3-year change in BMD. During 1 005 126 person-years of follow-up, 1500 hip fractures, 4881 forearm or wrist fractures, 2315 clinical spine fractures, and 21 247 total fractures occurred. The multivariate-adjusted hazard ratios for current PPI use were 1.00 (95% confidence interval [CI], 0.71-1.40) for hip fracture, 1.47 (95% CI, 1.18-1.82) for clinical spine fracture, 1.26 (95% CI, 1.05-1.51) for forearm or wrist fracture, and 1.25 (95% CI, 1.15-1.36) for total fractures. The BMD measurements did not vary between PPI users and nonusers at baseline. Use of PPIs was associated with only a marginal effect on 3-year BMD change at the hip (P = .05) but not at other sites. Use of PPIs was not associated with hip fractures but was modestly associated with clinical spine, forearm or wrist, and total fractures.", "Many patients receive prolonged proton pump inhibitor (PPI) therapy for upper gastrointestinal disorders, but the long-term safety of PPIs, particularly increased risk of hip and nonhip fractures, has been questioned. To summarize the current literature on the risk of bone mineral density (BMD) reduction and fracture associated with PPI therapy, we conducted a literature search to identify all pertinent studies from 1980-February 2011. A total of 14 observational studies were included in this review. Most studies evaluated the risk of fracture associated with prolonged PPI exposure. Eight studies found an increased fracture risk at the hip, and five studies found an increased fracture risk at the spine associated with PPIs. Three studies showed reduction in fracture risk associated with PPIs after discontinuation for 1 month-1 year. Three studies evaluated the risk of BMD reduction associated with PPIs but did not find consistent changes in baseline or subsequent BMD. The current data suggest a modest increase in the risk of hip fracture and vertebral fracture associated with PPIs, although some studies showed conflicting results. Further studies will be needed to determine whether the increased risk of fracture is due to PPI exposure or residual confounding.", "Proton pump inhibitors (PPIs) have been widely used since their introduction in the late 1980s because they are highly effective for acid-related conditions. However, some recent epidemiological studies have suggested a positive association between PPI therapy and the risk of osteoporotic fractures. The potential mechanisms underlying this association may be related to the physiologic effects of chronic acid suppression on calcium metabolism. First, chronic hypergastrinemia induced by PPI therapy may lead to parathyroid hyperplasia, resulting in increased loss of calcium from the bone. Second, profound gastric acid suppression may reduce the bioavailability of calcium for intestinal absorption. I will review the published evidence regarding these potential links and discuss their clinical implications.", "This review summarizes adverse effects of potential proton pump inhibitors (PPIs), including nutritional deficiencies (B12 and magnesium), rebound acid hypersecretion, acute interstitial nephritis, gastric carcinoid tumor, cardiovascular risk with clopidogrel and PPI coprescription, bone fractures, enteric infections and pneumonia. An epidemiologic framework is applied to assess clinical relevance and reinforce best practice recommendations. The evidence for PPI adverse events is limited by the absence of Level 1 (randomized controlled trial) studies. The best evidence supports Clostridium difficile and bone fractures in susceptible populations. A substantial reduction in gastrointestinal bleeding risk without increase in cardiovascular events was observed in the COGENT trial when clopidogrel was coprescribed with omeprazole. The risk of pneumonia is inconsistent, and although acute interstitial nephritis, nutritional deficiencies (including B12 and hypomagnesemia), gastric carcinoid and rebound hyperacidity are biologically plausible, studies have failed to demonstrate supportive clinical relevance. Prescribe PPI for robust indications only. Strong data supporting risk of adverse events are lacking; however, exercise caution in the elderly and in patients with other risk factors for bone fractures or C. difficile infection.", "To evaluate postoperative medical complications and the association between these complications and mortality at 30 days and one year after surgery for hip fracture and to examine the association between preoperative comorbidity and the risk of postoperative complications and mortality. Prospective observational cohort study. University teaching hospital. 2448 consecutive patients admitted with an acute hip fracture over a four year period. We excluded 358 patients: all those aged < 60; those with periprosthetic fractures, pathological fractures, and fractures treated without surgery; and patients who died before surgery. Routine care for hip fractures. Postoperative complications and mortality at 30 days and one year. Mortality was 9.6% at 30 days and 33% at one year. The most common postoperative complications were chest infection (9%) and heart failure (5%). In patients who developed postoperative heart failure mortality was 65% at 30 days (hazard ratio 16.1, 95% confidence interval 12.2 to 21.3). Of these patients, 92% were dead by one year (11.3, 9.1 to 14.0). In patients who developed a postoperative chest infection mortality at 30 days was 43% (8.5, 6.6 to 11.1). Significant preoperative variables for increased mortality at 30 days included the presence of three or more comorbidities (2.5, 1.6 to 3.9), respiratory disease (1.8, 1.3 to 2.5), and malignancy (1.5, 1.01 to 2.3). In elderly people with hip fracture, the presence of three or more comorbidities is the strongest preoperative risk factor. Chest infection and heart failure are the most common postoperative complications and lead to increased mortality. These groups offer a clear target for specialist medical assessment." ]
Whole-genome duplication and gene regulation in European grayling (Thymallus thymallus)	Whole-genome duplication (WGD) has been a major evolutionary driver of increased genomic complexity in vertebrates. One such event occurred in the salmonid family ∼80 Ma (Ss4R) giving rise to a plethora of structural and regulatory duplicate-driven divergence, making salmonids an exemplary system to investigate the evolutionary consequences of WGD. Here, we present a draft genome assembly of European grayling (Thymallus thymallus) and use this in a comparative framework to study evolution of gene regulation following WGD. Among the Ss4R duplicates identified in European grayling and Atlantic salmon (Salmo salar), one-third reflect nonneutral tissue expression evolution, with strong purifying selection, maintained over ∼50 Myr. Of these, the majority reflect conserved tissue regulation under strong selective constraints related to brain and neural-related functions, as well as higher-order protein-protein interactions. A small subset of the duplicates have evolved tissue regulatory expression divergence in a common ancestor, which have been subsequently conserved in both lineages, suggestive of adaptive divergence following WGD. These candidates for adaptive tissue expression divergence have elevated rates of protein coding- and promoter-sequence evolution and are enriched for immune- and lipid metabolism ontology terms. Lastly, lineage-specific duplicate divergence points toward underlying differences in adaptive pressures on expression regulation in the nonanadromous grayling versus the anadromous Atlantic salmon. Our findings enhance our understanding of the role of WGD in genome evolution and highlight cases of regulatory divergence of Ss4R duplicates, possibly related to a niche shift in early salmonid evolution.	[ "Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis- and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.", "Although gene duplication is widely believed to be the major source of genetic novelty, how the expression or regulatory network of duplicate genes evolves remains poorly understood. In this article, we propose an additive expression distance between duplicate genes, so that the evolutionary rate of expression divergence after gene duplication can be estimated through phylogenomic analysis. We have analyzed yeast genome sequences, microarrays, and transcriptional regulatory networks, showing a >10-fold increase in the initial rate for both expression and regulatory network evolution after gene duplication but only an approximately 20% rate increase in the early stage for protein sequences. Based on the estimated age distribution of yeast duplicate genes, we roughly estimate that the initial rate of expression divergence shortly after gene duplication is 2.9 x 10(-9) per year, whereas the baseline rate for very ancient gene duplication is 0.14 x 10(-9) per year. Relative expression rate tests suggest that the expression of duplicate genes tends to evolve asymmetrically, that is, the expression of one copy evolves rapidly, whereas the other one largely maintains the ancestral expression profile. Our study highlights the crucial role of early rapid evolution after gene/genome duplication for continuously increasing the complexity of the yeast regulatory network.", "Microarray technologies allow the identification of large numbers of expression differences within and between species. Although environmental and physiological stimuli are clearly responsible for changes in the expression levels of many genes, it is not known whether the majority of changes of gene expression fixed during evolution between species and between various tissues within a species are caused by Darwinian selection or by stochastic processes. We find the following: (1) expression differences between species accumulate approximately linearly with time; (2) gene expression variation among individuals within a species correlates positively with expression divergence between species; (3) rates of expression divergence between species do not differ significantly between intact genes and expressed pseudogenes; (4) expression differences between brain regions within a species have accumulated approximately linearly with time since these regions emerged during evolution. These results suggest that the majority of expression differences observed between species are selectively neutral or nearly neutral and likely to be of little or no functional significance. Therefore, the identification of gene expression differences between species fixed by selection should be based on null hypotheses assuming functional neutrality. Furthermore, it may be possible to apply a molecular clock based on expression differences to infer the evolutionary history of tissues.", "Gene duplication provides raw material for functional innovation. Recent advances have shed light on two fundamental questions regarding gene duplication: which genes tend to undergo duplication? And how does natural selection subsequently act on them? Genomic data suggest that different gene classes tend to be retained after single-gene and whole-genome duplications. We also know that functional differences between duplicate genes can originate in several different ways, including mutations that directly impart new functions, subdivision of ancestral functions and selection for changes in gene dosage. Interestingly, in many cases the 'new' function of one copy is a secondary property that was always present, but that has been co-opted to a primary role after the duplication.", "Thirty years after Susumu Ohno proposed that vertebrate genomes are degenerate polyploids, the extent to which genome duplication contributed to the evolution of the vertebrate genome, if at all, is still uncertain. Sequence-level studies on model organisms whose genomes show clearer evidence of ancient polyploidy are invaluable because they indicate what the evolutionary products of genome duplication can look like. The greatest mystery is the molecular basis of diploidization, the evolutionary process by which a polyploid genome turns into a diploid one.", "Twelve populations of Escherichia coli, derived from a common ancestor, evolved in a glucose-limited medium for 20,000 generations. Here we use DNA expression arrays to examine whether gene-expression profiles in two populations evolved in parallel, which would indicate adaptation, and to gain insight into the mechanisms underlying their adaptation. We compared the expression profile of the ancestor to that of clones sampled from both populations after 20,000 generations. The expression of 59 genes had changed significantly in both populations. Remarkably, all 59 were changed in the same direction relative to the ancestor. Many of these genes were members of the cAMP-cAMP receptor protein (CRP) and guanosine tetraphosphate (ppGpp) regulons. Sequencing of several genes controlling the effectors of these regulons found a nonsynonymous mutation in spoT in one population. Moving this mutation into the ancestral background showed that it increased fitness and produced many of the expression changes manifest after 20,000 generations. The same mutation had no effect on fitness when introduced into the other evolved population, indicating that a mutation of similar effect was present already. Our study demonstrates the utility of expression arrays for addressing evolutionary issues including the quantitative measurement of parallel evolution in independent lineages and the identification of beneficial mutations.", "Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/." ]
Multiply injured child: a unique challenge to the medical community	Multiply injured child is a unique challenge to the medical communities worldwide. It is a leading cause of preventable mortality and morbidity in children. Common skeletal injuries include closed or open fractures of tibia and femur and pelvic injuries. Initial management focuses on saving life and then saving limb as per pediatric advanced life support and advanced trauma life support. Orthopedic management of open fracture includes splinting the limb, administration of prophylactic antibiotic, and surgical debridement of the wound when safe. However, gross contamination, compartment syndrome, and vascular injuries demand urgent attention.	[ "A study was undertaken to determine what factors are important in determining whether or not a patient with an open fracture will develop an infection. Debrided tissue was cultured to determine quantitative bacterial counts. The patients' subsequent records were evaluated and the infection rate correlated with culture data and other factors that might be associated with development of infection. Of the 70 patients evaluated, 13 (19%) became infected. When the infection rate was correlated with the use of fixation devices, it was found that 1/19 (5%) of the patients with no implants, 3/16 (19%) of the patients with external fixation devices, and 9/35 (26%) of the patients with internal fixation became infected. Most of the infections were caused by Gram-negative bacteria. There was little correlation between the bacterial counts in the first piece of tissue taken at debridement and the development of infection. There was significant correlation between the bacterial count in the last piece of tissue taken at debridement and the development of infection. Thus the infection was correlated with what was in the tissue when the patient left the operating room and not with what was in the tissue when the patient entered the operating room.", "Open fractures are considered orthopedic emergencies that are traditionally treated with surgical debridement within 6 h of injury to prevent infection. However, this proclaimed \"6-h rule\" is arbitrary and not based on rigorous scientific evidence. The aim of our study was to systematically review the literature that compares late (>6 h from the time of injury) to early (<6 h from the time of injury) surgical debridement of pediatric open fractures. We searched several databases from 1946 to 2013 for any observational or experimental studies that evaluated late and early surgical debridement of pediatric open fractures. We performed a meta-analysis using a random effects model to pool odds ratios for a comparison of infection rates between children undergoing late versus early surgical debridement. We also investigated the infection rates in upper- and lower-limb pediatric open fractures. Descriptive, quantitative, and qualitative data were extracted. Of the 12 articles identified, three studies (retrospective cohort studies) were eligible for the meta-analysis, encompassing a total of 714 open fractures. The pooled odds ratio (OR = 0.79) for infection between late and early surgical debridement was in favor of late surgical debridement but was not statistically significant (95 % CI 0.32, 1.99; p = 0.38, I (2) = 0 %). No significant difference in infection rate was detected between pediatric open fractures in the upper and lower limbs according to the time threshold in the included studies (OR = 0.72, 95 % CI 0.29, 1.82; p = 0.40, I (2) = 0 %). The cumulative evidence does not, at present, indicate an association between late surgical debridement and higher infection rates in pediatric open fractures. However, initial expedient surgical debridement of open fractures in children should always remain the rule. Thus, multi-center randomized controlled trials or prospective cohort studies will be able to answer this question with more certainty and a higher level of evidence. Level III.", "Following the introduction of national standards in 2009, most major paediatric trauma is now triaged to specialist units offering combined orthopaedic and plastic surgical expertise. We investigated the management of open tibia fractures at a paediatric trauma centre, primarily reporting the risk of infection and rate of union. A retrospective review was performed on 61 children who between 2007 and 2015 presented with an open tibia fracture. Their mean age was nine years (2 to 16) and the median follow-up was ten months (interquartile range 5 to 18). Management involved IV antibiotics, early debridement and combined treatment of the skeletal and soft-tissue injuries in line with standards proposed by the British Orthopaedic Association. There were 36 diaphyseal fractures and 25 distal tibial fractures. Of the distal fractures, eight involved the physis. Motor vehicle collisions accounted for two thirds of the injuries and 38 patients (62%) arrived outside of normal working hours. The initial method of stabilisation comprised: casting in nine cases (15%); elastic nailing in 19 (31%); Kirschner (K)-wiring in 13 (21%); intramedullary nailing in one (2%); open reduction and plate fixation in four (7%); and external fixation in 15 (25%). Wound management comprised: primary wound closure in 24 (39%), delayed primary closure in 11 (18%), split skin graft (SSG) in eight (13%), local flap with SSG in 17 (28%) and a free flap in one. A total of 43 fractures (70%) were Gustilo-Anderson grade III. There were four superficial (6.6%) and three (4.9%) deep infections. Two deep infections occurred following open reduction and plate fixation and the third after K-wire fixation of a distal fracture. No patient who underwent primary wound closure developed an infection. All the fractures united, although nine patients required revision of a mono-lateral to circular frame for delayed union (two) or for altered alignment or length (seven). The mean time to union was two weeks longer in diaphyseal fractures than in distal fractures (13 weeks versus 10.8 weeks, p = 0.016). Children aged > 12 years had a significantly longer time to union than those aged < 12 years (16.3 weeks versus 11.4 weeks, p = 0.045). The length of stay in hospital for patients with a Gustilo-Anderson grade IIIB fracture was twice as long as for less severe injuries. Fractures in children heal better than those in adults. Based on our experience of deep infection we discourage the use of internal fixation with a plate for open tibial fractures in children. We advocate aggressive initial wound debridement in theatre with early definitive combined orthopaedic and plastic surgery in order to obtain skeletal stabilisation and soft-tissue cover. Cite this article: Bone Joint J 2017;99-B:544-53.", "Statistical tests for funnel-plot asymmetry are common in meta-analyses. Inappropriate application can generate misleading inferences about publication bias. We aimed to measure, in a survey of meta-analyses, how frequently the application of these tests would be not meaningful or inappropriate. We evaluated all meta-analyses of binary outcomes with é 3 studies in the Cochrane Database of Systematic Reviews (2003, issue 2). A separate, restricted analysis was confined to the largest meta-analysis in each of the review articles. In each meta-analysis, we assessed whether criteria to apply asymmetry tests were met: no significant heterogeneity, I2 < 50%, é 10 studies (with statistically significant results in at least 1) and ratio of the maximal to minimal variance across studies > 4. We performed a correlation and 2 regression asymmetry tests and evaluated their concordance. Finally, we sampled 60 meta-analyses from print journals in 2005 that cited use of the standard regression test. A total of 366 of 6873 (5%) and 98 of 846 meta-analyses (12%) in the wider and restricted Cochrane data set, respectively, would have qualified for use of asymmetry tests. Asymmetry test results were significant in 7%-18% of the meta-analyses. Concordance between the 3 tests was modest (estimated k 0.33-0.66). Of the 60 journal meta-analyses, 7 (12%) would qualify for asymmetry tests; all 11 claims for identification of publication bias were made in the face of large and significant heterogeneity. Statistical conditions for employing asymmetry tests for publication bias are absent from most meta-analyses; yet, in medical journals these tests are performed often and interpreted erroneously.", "This study is a single center retrospective chart and radiographic review of patients with open tibia fractures under the age of 16 years of age over past 10 years. The purpose of this study is to investigate the treatment of open pediatric tibia fractures with plating in regards to time to ambulation, time to union, and deformity in comparison to other treatment options. We found that plating open pediatric tibia fractures is a safe treatment option that can lead to excellent results with low risk of complications.", "We evaluated retrospectively the treatment of 44 open femur fractures occurring between the lesser trochanter and the distal femoral physis in 43 children aged 16 years and younger. Fractures that involved the physis or that were a consequence of gunshot wounds were excluded. There were 25 grade I, 9 grade II, and 9 grade III fractures. The mean age at injury was 9.5 years. Ninety percent of the fractures were automobile related. More than 70% of the children had associated injuries. The average time to healing for all fractures in this study was 17 weeks. Our data indicate that there is a statistically significant increased time to heal with increasing age of the child (p = 0.04). Additionally, grade III fractures healed more slowly than grade I or II fractures (p = 0.0006). Fractures treated with external fixation took longer to unite than those treated with other methods (p = 0.05). The presence of complications increased the time to fracture union (p = 0.00001). Grade III injuries were the most difficult to manage; 50% of the fractures in this group developed osteomyelitis and 20% malunited. In contrast, none of the fractures in either the grade I or II groups developed deep infection. After aggressive debridement, grade I and grade II fractures may be stabilized with age-appropriate fixation methods. Grade III injuries should be managed with vigorous debridement and vigilance, as these injuries are prone to deep infection and malunion. The optimal method of skeletal stabilization in grade III fractures remains unresolved.", "We reviewed the results of treatment of forty open diaphyseal fractures of the lower extremity in thirty-five children. The patients were between three and sixteen years old, and they had been managed between 1980 and 1988. The minimum duration of follow-up was one year. Eighty-six per cent of the patients had been injured in a motor-vehicle accident, and 74 per cent had associated injuries. Thirty-one of the fractures were Grade-II open or Grade-III open and seven were Grade-I open, according to the classification of Gustilo and Anderson. Two patients who had initially had a closed fracture were treated with a fasciotomy for a compartment syndrome, so these two fractures were included as open. Four other patients who had a Grade-II or III open fracture also needed a fasciotomy. All wounds were treated with immediate and repeat débridement and early soft-tissue coverage. Twenty-two fractures healed primarily. There were three early amputations. Twelve fractures that healed after six months were classified as delayed unions and three fractures were classified as non-unions because of the absence or arrest of healing, as seen on serial roentgenograms. Additional intervention was used to achieve union of eight of the fifteen fractures that had been classified as a delayed union or a non-union. Ten of the forty fractures were associated with infection, but osteomyelitis developed in only one patient. No patient had a growth arrest. Only one patient had a limb-length discrepancy that was more than two centimeters. Three early amputations and one delayed amputation were performed in patients who had a Grade-IIIC open fracture." ]
AgBioData: Agricultural Biodata Management	The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database products that are more Findable, Accessible, Interoperable and Reusable. We strive to promote authentic, detailed, accurate and explicit communication between all parties involved in scientific data. As a step toward this goal, we present the current state of biocuration, ontologies, metadata and persistence, database platforms, programmatic (machine) access to data, communication and sustainability with regard to data curation. Each section describes challenges and opportunities for these topics, along with recommendations and best practices.	[ "The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available; database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions. This study examines the finances and use statistics of a few of these organizations in more depth, and reviews several economic models that may help sustain them. Six organizations were studied. Their administrative overhead is fairly low; non-administrative personnel and computer-related costs account for 77% of expenses. One smaller, more specialized US database, in 1997, had 60% of total access from US domains; a majority (56%) of its US accesses came from commercial domains, although only 2% of the 153 databases originally studied received any industrial support. The most popular model used to gain industrial support is asymmetric pricing: preferentially charging the commercial users of a database. At least five biological databases have recently begun using this model. Advertising is another model which may be useful for the more general, more heavily used sites. Microcommerce has promise, especially for databases that do not attract advertisers, but needs further testing. The least income reported for any of the databases studied was $50,000/year; applying this rate to 400 biological databases (a lower limit of the number of such databases, many of which require far larger resources) would mean annual support need of at least $20 million. To obtain this level of support is challenging, yet failure to accept the challenge could be catastrophic. lynda@tc.umn. edu", "Databases and data repositories provide essential functions for the research community by integrating, curating, archiving and otherwise packaging data to facilitate discovery and reuse. Despite their importance, funding for maintenance of these resources is increasingly hard to obtain. Fueled by a desire to find long term, sustainable solutions to database funding, staff from the Arabidopsis Information Resource (TAIR), founded the nonprofit organization, Phoenix Bioinformatics, using TAIR as a test case for user-based funding. Subscription-based funding has been proposed as an alternative to grant funding but its application has been very limited within the nonprofit sector. Our testing of this model indicates that it is a viable option, at least for some databases, and that it is possible to strike a balance that maximizes access while still incentivizing subscriptions. One year after transitioning to subscription support, TAIR is self-sustaining and Phoenix is poised to expand and support additional resources that wish to incorporate user-based funding strategies. Database URL: www.arabidopsis.org.", "Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species.", "We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search.", "The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP.", "The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository.", "Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC) step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD) and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Our semi-automated pipeline hyperlinks articles published in GENETICS to model organism databases such as WormBase. Our pipeline results in interactive articles that are data rich with high accuracy. The use of a manual quality control step sets this pipeline apart from other hyperlinking tools and results in benefits to authors, journals, readers and databases.", "Kyoto Encyclopedia of Genes and Genomes (KEGG, http://www.genome.jp/kegg/ or http://www.kegg.jp/) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem. Major efforts have been undertaken to manually create a knowledge base for such systemic functions by capturing and organizing experimental knowledge in computable forms; namely, in the forms of KEGG pathway maps, BRITE functional hierarchies and KEGG modules. Continuous efforts have also been made to develop and improve the cross-species annotation procedure for linking genomes to the molecular networks through the KEGG Orthology system. Here we report KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets. We also report a variant of the KEGG mapping procedure to extend the knowledge base, where different types of data and knowledge, such as disease genes and drug targets, are integrated as part of the KEGG molecular networks. Finally, we describe recent enhancements to the KEGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.", "As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net.", "Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops and a community resource for rice. We are populating and curating Gramene with annotated rice (Oryza sativa) genomic sequence data and associated biological information including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait Loci (QTL). In order to support queries across various data sets as well as across external databases, Gramene will employ three related controlled vocabularies. The specific goal of Gramene is, first to provide a Trait Ontology (TO) that can be used across the cereal crops to facilitate phenotypic comparisons both within and between the genera. Second, a vocabulary for plant anatomy terms, the Plant Ontology (PO) will facilitate the curation of morphological and anatomical feature information with respect to expression, localization of genes and gene products and the affected plant parts in a phenotype. The TO and PO are both in the early stages of development in collaboration with the International Rice Research Institute, TAIR and MaizeDB as part of the Plant Ontology Consortium. Finally, as part of another consortium comprising macromolecular databases from other model organisms, the Gene Ontology Consortium, we are annotating the confirmed and predicted protein entries from rice using both electronic and manual curation." ]
Roles of Rab3A in hepatocellular carcinoma	Rab3A is a small Ras-like GTPase critical for membrane traffic. Although the functions of Rab3A have been reported in several cancers, the roles of Rab3A in hepatocellular carcinoma (HCC) have never been determined. To investigate the potential roles of Rab3A in HCC progression, we first determined Rab3A levels in HCC tissues and observed upregulated mRNA and protein levels of Rab3A in most tumor tissues. However, in vitro data showed that decreasing Rab3A in most HCC cell lines conferred no significant effects and overexpressing Rab3A in PLC/PRF/5 cells even inhibited migration and invasion. Meanwhile, the upregulation of Rab3A in HCC patients did not correlate with metastasis or overall survival of HCC patients. These contradict data suggested that Rab3A might act as metastatic suppressor and its effects might be attenuated in most HCC cells. Further experiments revealed that O-GlcNAcylation on Rab3A was key for attenuating Rab3A-mediated effects by regulating its GTP-binding activity, and verified the effects of Rab3A and its aberrant O-GlcNAcylation on HCC metastasis in vitro and in vivo. We also found that Rab3A and its O-GlcNAcylation had opposite roles in mitochondria oxidative phosphorylation (mtOXPHOS), and their functions on HCC metastasis were partially depended on their effects on metabolic reprogramming.	[ "The Rab3 proteins are monomeric GTP-binding proteins associated with secretory vesicles. In their active GTP-bound state, Rab3 proteins are involved in the regulation of hormone secretion and neurotransmitter release. This action is thought to involve specific effectors, including two Ca2+-binding proteins, Rabphilin and Rim. Rab3 acts late in the exocytotic process, in a cell domain in which the intracellular Ca2+ concentration is susceptible to rapid changes. Therefore, we examined the possible Ca2+-dependency of the regulatory action of GTP-bound Rab3 and wild-type Rab3 on neuroexocytosis at identified cholinergic synapses in Aplysia californica. The effects of recombinant GTPase-deficient Aplysia-Rab3 (apRab3-Q80L) or wild-type apRab3 were studied on evoked acetylcholine release. Intraneuronal application of apRab3-Q80L in identified neurons of the buccal ganglion of Aplysia led to inhibition of neurotransmission; wild-type apRab3 was less effective. Intracellular chelation of Ca2+ ions by EGTA greatly potentiated the inhibitory action of apRab3-Q80L. Train and paired-pulse facilitation, two Ca2+-dependent forms of short-term plasticity induced by a rise in intraterminal Ca2+ concentration, were increased after injection of apRab3-Q80L. This result suggests that the inhibition exerted by GTP-bound Rab3 on neuroexocytosis is reduced during transient augmentations of intracellular Ca2+ concentration. Therefore, a Ca2+-dependent modulation of GTP-bound Rab3 function may contribute to short-term plasticity.", "The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.", "Rab3A is expressed predominantly in brain and synaptic vesicles. Rab3A is involved specifically in tethering and docking of synaptic vesicles prior to fusion which is a critical step in regulated release of neurotransmitters. The precise function of Rab3A is still not known. However, up-regulation of Rab3A has been reported in malignant neuroendocrine and breast cancer cells. In the present study, the structure of Rab3A protein was generated using MODELLER 9v8 software. The modeled protein structure was validated and subjected to molecular docking analyses. Docking with GTP was carried out on the binding site of Rab3A using GOLD software. The Rab3A-GTP complex has best GOLD fitness value of 77.73. Ligplot shows hydrogen bondings (S16, S17, V18, G19, K20, T21, S22, S31, T33, A35, S38, T39 and G65) and hydrophobic interacting residues (F25, F32, P34, F36, V37, D62 and A64) with the GTP ligands in the binding site of Rab3A protein. Here, the ligand molecules of NCI diversity set II from the ZINC database against the active site of the Rab3A protein were screened. For this purpose, the incremental construction algorithm of GLIDE and the genetic algorithm of GOLD were used. Docking results were analyzed for top ranking compounds using a consensus scoring function of X-Score to calculate the binding affinity and Ligplot was used to measure protein-ligand interactions. Five compounds which possess good inhibitory activity and may act as potential high affinity inhibitors against Rab3A active site were identified. The top ranking molecule (ZINC13152284) has a Glide score of -6.65 kcal/mol, X-Score of -3.02 kcal/mol and GOLD score of 64.54 with 03 hydrogen bonds and 09 hydrophobic contacts. This compound is thus a good starting point for further development of strong inhibitors.", "Synaptic vesicle exocytosis occurs in consecutive steps: docking, which specifically attaches vesicles to the active zone; priming, which makes the vesicles competent for Ca(2+)-triggered release and may involve a partial fusion reaction; and the final Ca(2+)-regulated step that completes fusion. Recent evidence suggests that the critical regulation of the last step in the reaction is mediated by two proteins with opposite actions: synaptotagmin, a Ca(2+)-binding protein that is essential for Ca(2+)-triggered release and probably serves as the Ca(2+)-sensor in fusion, and rab3, which limits the number of vesicles that can be fused as a function of Ca2+ in order to allow a temporally limited, repeatable signal." ]
what are waxes in plants?	Cuticle waxes, which are primarily comprised of very-long-chain (VLC) alkanes, play an important role in plant reproductive development.	[ "The nucleotide sequence of the autonomous transposable element En-1 isolated from the wx-844::En-1 allele has been determined. En-1 is 8287 bp long. The structure of the mosaic gene 1, coding for the major En transcript, has been established. The promoter gene 1 is located in the highly structured left end of the element and the gene spans almost the entire length of En-1. The first intron of gene 1 is 4434 nucleotides long and contains two large open reading frames, 2714 bp and 761 bp in size, which hybridize to minor RNA species in Northern blot experiments.", "Three semidominant, nonallelic mutations of maize, Teopod 1 (Tp1), Teopod 2 (Tp2) and Teopod 3 (Tp3), have a profound effect on both vegetative and reproductive development. Although each mutation is phenotypically distinct, they all (1) increase the number of vegetative phytomers; (2) increase the number of phytomers producing ears, tillers and prop roots; (3) increase the number of leaves bearing epidermal wax; (4) decrease the size of leaves and internodes; (5) decrease the size of both the ear and tassel; and (6) transform reproductive structures into vegetative ones. The analysis presented here suggests that this phenotype reflects the prolonged expression of a juvenile, vegetative developmental program which overlaps with the reproductive developmental program. The expression of these mutations is different in each of the four inbred backgrounds used in this study. Tp1 and Tp2 have similar phenotypes and are more highly expressed in the A632 and Oh51a inbred backgrounds than in W23 and Mo17. Tp3 has less extreme effects than either of these mutations and has the opposite modification pattern; i.e., it is more highly expressed in W23 and Mo17 than in A632 and Oh51a. The expression of Tp1 and Tp2 in the presence of varying doses of their wild-type alleles indicate that both are gain-of-function mutations. The phenotypes of Tp1 and Tp2 and the nature of their response to variation in gene dose suggest that they control related, but nonidentical functions. The developmental and evolutionary implications of the heterochronic phenotype of these mutations is discussed.", "We have identified a new Arabidopsis mutant, yore-yore (yre), which has small trichomes and glossy stems. Adhesion between epidermal cells was observed in the organs of the yre shoot. The cloned YRE had high homology to plant genes involved in epicuticular wax synthesis, such as ECERIFERUM1 (CER1) and maize GLOSSY1. The phenotype of transgenic plants harboring double-stranded RNA interference (dsRNAi) YRE was quite similar to that of the yre mutant. The amount of epicuticular wax extracted from leaves and stems of yre-1 was approximately one-sixth of that from the wild type. YRE promoter::GUS and in situ hybridization revealed that YRE was specifically expressed in cells of the L1 layer of the shoot apical meristem and young leaves, stems, siliques, and lateral root primordia. Strong expression was detected in developing trichomes. The trichome structure of cer1 was normal, whereas that of the yre cer1 double mutant was heavily deformed, indicating that epicuticular wax is required for normal growth of trichomes. Double mutants of yre and trichome-morphology mutants, glabra2 (gl2) and transparent testa glabra1 (ttg1), showed that the phenotype of the trichome structure was additive, suggesting that the wax-requiring pathway is distinct from the trichome development pathway controlled by GL2 and TTG1.", "To learn more about the role of the CER6 condensing enzyme in Arabidopsis surface wax production, we determined CER6 transcription domains and the timing of CER6 transcription in vegetative and reproductive structures from juvenile, mature, and senescing tissues. We found that CER6 is highly transcribed throughout development, exclusively in the epidermal cells in all tissues examined. The only exception to the epidermal expression was observed in anthers nearing maturity, in which CER6 mRNA was localized in the tapetum. To determine if environmental factors such as light and water deficit, which are known to stimulate wax accumulation, induce CER6 transcription, we examined the effects of these factors on CER6 transcript abundance. Our results demonstrate that light is essential for CER6 transcription, and that osmotic stress and the presence of abscisic acid enhance CER6 transcript accumulation. CER6 promoter-directed expression of the beta-glucuronidase reporter gene in transgenic plants demonstrated that the CER6 promoter was highly effective in directing epidermis-specific expression in Arabidopsis and tobacco (Nicotiana tabacum). Furthermore, CER6 promoter-driven CER6 overexpression resulted in increased wax deposition in Arabidopsis stems. These experiments indicate that the expression level of CER6 in the epidermis is one of the factors controlling wax accumulation on Arabidopsis stems.", "The cuticle covering the aerial organs of land plants plays a protective role against several biotic and abiotic stresses and, in addition, participates in a variety of plant-insect interactions. Here, we describe the molecular cloning and characterization of the maize (Zea mays) GLOSSY1 (GL1) gene, a component of the pathway leading to cuticular wax biosynthesis in seedling leaves. The genomic and cDNA sequences we isolated differ significantly in length and in most of the coding region from those previously identified. The predicted GL1 protein includes three histidine-rich domains, the landmark of a family of membrane-bound desaturases/hydroxylases, including fatty acid-modifying enzymes. GL1 expression is not restricted to the juvenile developmental stage of the maize plant, pointing to a broader function of the gene product than anticipated on the basis of the mutant phenotype. Indeed, in addition to affecting cuticular wax biosynthesis, gl1 mutations have a pleiotropic effect on epidermis development, altering trichome size and impairing cutin structure. Of the many wax biosynthetic genes identified so far, only a few from Arabidopsis (Arabidopsis thaliana) were found to be essential for normal cutin formation. Among these is WAX2, which shares 62% identity with GL1 at the protein level. In wax2-defective plants, cutin alterations induce postgenital organ fusion. This trait is not displayed by gl1 mutants, suggesting a different role of the maize and Arabidopsis cuticle in plant development.", "The protective wax coating on plant surfaces has long been considered to be non-uniform in composition at a subcellular scale. In recent years, direct evidence has started to accumulate showing quantitative compositional differences between the epicuticular wax (i.e. wax exterior to cutin that can be mechanically peeled off) and intracuticular wax (i.e. wax residing within the mechanically resistant layer of cutin) layers in particular. This review provides a first synthesis of the results acquired for all the species investigated to date in order to assign chemical information directly to cuticle substructures, together with an overview of the methods used and a discussion of possible mechanisms and biological functions. The development of methods to probe the wax for z-direction heterogeneity began with differential solvent extractions. Further research employing mechanical wax removal by adhesives permitted the separation and analysis of the epicuticular and intracuticular wax. In wild-type plants, the intracuticular (1-30 μg cm(-2)) plus the epicuticular wax (5-30 μg cm(-2)) combined to a total of 8-40 μg cm(-2). Cyclic wax constituents, such as triterpenoids and alkylresorcinols, preferentially or entirely accumulate within the intracuticular layer. Within the very-long-chain aliphatic wax components, primary alcohols tend to accumulate to higher percentages in the intracuticular wax layer, while free fatty acids and alkanes in many cases accumulate in the epicuticular layer. Compounds with different chain lengths are typically distributed evenly between the layers. The mechanism causing the fractionation remains to be elucidated but it seems plausible that it involves, at least in part, spontaneous partitioning due to the physico-chemical properties of the wax compounds and interactions with the intracuticular polymers. The arrangement of compounds probably directly influences cuticular functions.", "Most studies evaluating the effects of high-intensity drive-train (S1) stimulation on the measurement of the ventricular effective refractory period (VERP) demonstrated a shortening of the VERP. Because this effect may be due to the local release of catecholamines, VERP shortening would be expected to occur only near the site of stimulation. Local shortening in the VERP should then result in an increased dispersion of refractoriness during high-intensity drive-train stimulation. Thus, this study evaluated the spatial distribution of the VERP shortening resulting from high-intensity S1 stimulation and its effect on dispersion of refractoriness. Three groups of patients were studied. In group 1, 10 subjects without structural heart disease had VERP determinations performed at the right ventricular apex (RVA) and outflow tract (RVOT) while the S1 site was changed to evaluate the effects of low-intensity S1 stimulation on the measured VERP. In group 2, the effect of high-intensity S1 stimulation on the VERP was studied 0, 7, 14, and 21 mm away from the S1 site to measure the spatial distribution of VERP shortening and the effect on dispersion of refractoriness; 10 additional subjects without structural heart disease made up group 2. Because increased dispersion of refractoriness may be deleterious in certain clinical situations, the effect of high-intensity S1 stimulation was studied in group 3, which comprised 10 subjects with chronically implanted transvenous defibrillators; noninvasive measurements of the VERP through the chronic lead were made while the S1 stimulus intensity was varied from low to high intensity. All VERP determinations were performed during continuous pacing by use of an incremental method and a low stimulus intensity for the extrastimulus. In group 1, the RVA VERPs were 218 +/- 9 and 214 +/- 10 ms when the S1 site was the RVA and RVOT, respectively (P = NS). The RVOT VERPs were also unchanged when the S1 site was changed from the RVOT to the RVA. In group 2, high-intensity S1 changed the VERP from 224 +/- 8 (at twice the threshold) to 203 +/- 10 ms (P < .01), 220 +/- 11 to 209 +/- 12 ms (P < .01), 222 +/- 12 to 221 +/- 12 ms, and 220 +/- 11 to 221 +/- 11 ms at 0, 7, 14, and 21 mm away from the S1 site, respectively. High-intensity S1 stimulation led to an increase in the dispersion of refractoriness from 13 +/- 4 to 22 +/- 9 ms (P = .006). In group 3, high-intensity S1 stimulation shortened the VERP from 309 +/- 23 to 285 +/- 30 ms (P = .0003). Low-intensity S1 stimulation has no significant effect on the VERP. High-intensity S1 stimulation shortens the refractory period maximally at the site of stimulation; the VERP shortening dissipates between 7 and 14 mm away from the site of S1 stimulation, resulting in an increased dispersion of refractoriness. The local VERP shortening with high-intensity stimulation is noted in patients with chronically implanted defibrillator leads, which may have implications for the mechanism of proarrhythmia during high-intensity stimulation." ]
Early diagnosis and progression risk factors for interstitial lung disease in systemic sclerosis	Interstitial lung disease (ILD) is a group of lung diseases characterized by thickening of the interstitium surrounding pulmonary alveolar walls. It is related to specific radiographic features in lung imaging and/or the presence of restrictive disorders in pulmonary function tests (PFTs). ILD is one of the leading causes of death in systemic sclerosis patients. Major risk factors of ILD associated with SSc (SSc-ILD) include male sex, diffuse type of cutaneous SSc and presence of anti-Scl-70 antibodies. SSc-ILD is challenging to diagnose at an early stage as the symptoms are non-specific. The greatest risk of its development is during the 4-5 years after the initial diagnosis of systemic sclerosis. Clinical vigilance at the time, including regular pulmonary function tests and/or high-resolution com-puted tomography (HRCT), is needed. The aim of this paper is to summarize the current knowledge on early diagnostic methods and progression risk factors for SSc-ILD.	[ "We sought to determine the effectiveness of mycophenolate mofetil (MMF) in scleroderma- associated interstitial lung disease (SSc-ILD). We retrospectively identified patients who met criteria for systemic sclerosis, had evidence of SSc-ILD on chest CT, received > 1 g/d of MMF for >or= 6 months, and had pulmonary function data available. Vital capacity (VC) and diffusion capacity of the lung for carbon monoxide (Dlco) at treatment onset were compared with VC and Dlco values 12 months before and 12 months after treatment onset. Twelve-month values were imputed from regression lines generated using all VC and Dlco measurements made in the 24-month period either prior to or following treatment onset. Among 13 patients who met inclusion criteria, MMF was associated with a significant improvement in VC (mean, + 159 mL; confidence interval [CI], + 30 to + 289 mL; and + 4% of the predicted normal value; CI, + 2 to + 7%) after 12 months of treatment. In contrast, patients had a significant decrease in VC (mean, - 239 mL; CI, - 477 to - 0.5 mL; and - 5% of the predicted normal value; CI, - 11 to - 0.3%) in the 12 months prior to MMF treatment. Dlco did not change significantly during MMF treatment (mean, + 1% of the predicted normal value; CI, - 2 to + 5%) but decreased significantly in the 12 months prior to treatment (mean, - 5% of the predicted normal value; CI, - 10 to - 1%). These retrospective data suggest MMF improves VC in patients with SSc-ILD.", "12 months of oral cyclophosphamide has been shown to alter the progression of scleroderma-related interstitial lung disease when compared with placebo. However, toxicity was a concern and without continued treatment the efficacy disappeared by 24 months. We hypothesised that a 2 year course of mycophenolate mofetil would be safer, better tolerated, and produce longer lasting improvements than cyclophosphamide. This randomised, double-blind, parallel group trial enrolled patients from 14 US medical centres with scleroderma-related interstitial lung disease meeting defined dyspnoea, pulmonary function, and high-resolution CT (HRCT) criteria. The data coordinating centre at the University of California, Los Angeles (UCLA, CA, USA), randomly assigned patients using a double-blind, double-dummy, centre-blocked design to receive either mycophenolate mofetil (target dose 1500 mg twice daily) for 24 months or oral cyclophosphamide (target dose 2·0 mg/kg per day) for 12 months followed by placebo for 12 months. Drugs were given in matching 250 mg gel capsules. The primary endpoint, change in forced vital capacity as a percentage of the predicted normal value (FVC %) over the course of 24 months, was assessed in a modified intention-to-treat analysis using an inferential joint model combining a mixed-effects model for longitudinal outcomes and a survival model to handle non-ignorable missing data. The study was registered with ClinicalTrials.gov, number NCT00883129. Between Sept 28, 2009, and Jan 14, 2013, 142 patients were randomly assigned to either mycophenolate mofetil (n=69) or cyclophosphamide (n=73). 126 patients (mycophenolate mofetil [n=63] and cyclophosphamide [n=63]) with acceptable baseline HRCT studies and at least one outcome measure were included in the primary analysis. The adjusted % predicted FVC improved from baseline to 24 months by 2·19 in the mycophenolate mofetil group (95% CI 0·53-3·84) and 2·88 in the cyclophosphamide group (1·19-4·58). The course of the % FVC did not differ significantly between the two treatment groups based on the prespecified primary analysis using a joint model (p=0·24), indicating that the trial was negative for the primary endpoint. However, in a post-hoc analysis of the primary endpoint, the within-treatment change from baseline to 24 months derived from the joint model showed that the % FVC improved significantly in both the mycophenolate mofetil and cyclophosphamide groups. 16 (11%) patients died (five [7%] mycophenolate mofetil and 11 [15%] cyclophosphamide), with most due to progressive interstitial lung disease. Leucopenia (30 patients vs four patients) and thrombocytopenia (four vs zero) occurred more often in patients given cyclophosphamide than mycophenolate mofetil. Fewer patients on mycophenolate mofetil than on cyclophosphamide prematurely withdrew from study drug (20 vs 32) or met prespecified criteria for treatment failure (zero vs two). The time to stopping treatment was shorter in the cyclophosphamide group (p=0·019). Treatment of scleroderma-related interstitial lung disease with mycophenolate mofetil for 2 years or cyclophosphamide for 1 year both resulted in significant improvements in prespecified measures of lung function over the 2 year course of the study. Although mycophenolate mofetil was better tolerated and associated with less toxicity, the hypothesis that it would have greater efficacy at 24 months than cyclophosphamide was not confirmed. These findings support the potential clinical effectiveness of both cyclophosphamide and mycophenolate mofetil for progressive scleroderma-related interstitial lung disease, and the present preference for mycophenolate mofetil because of its better tolerability and toxicity profile. National Heart, Lung and Blood Institute, National Institutes of Health; with drug supply provided by Hoffmann-La Roche and Genentech.", "Transforming growth factor β (TGFβ) and platelet-derived growth factor (PDGF) may play a critical role in systemic sclerosis (SSc)-related interstitial lung disease (ILD), and imatinib is a potent inhibitor of TGFβ and PDGF production. In this 1-year, phase I/IIa open-label pilot study of imatinib in patients with SSc-related active ILD, our primary aim was to assess the safety of imatinib; we also explored its efficacy. We recruited 20 SSc patients with a forced vital capacity (FVC) of <85% predicted, dyspnea on exertion, and presence of a ground-glass appearance on high-resolution computed tomography. Patients received oral therapy with imatinib (up to 600 mg/day) for a period of 1 year. Adverse events were recorded, pulmonary function was tested, and the modified Rodnan skin thickness score (MRSS) was assessed every 3 months. The course of changes in lung function, the Health Assessment Questionnaire (HAQ) disability index (DI), and the MRSS were modeled over the period of study to explore treatment efficacy. The majority of patients were female (65%), Caucasian (75%), and had diffuse cutaneous SSc (70%). At baseline, the mean ± SD FVC % predicted was 65.2 ± 14.0 and the mean ± SD MRSS was 18.7 ± 10.1. The mean ± SD dosage of imatinib was 445 ± 125 mg/day. Of the 20 SSc patients, 12 completed the study, 7 discontinued because of adverse events (AEs), and 1 patient was lost to followup. Common AEs (≥20%) included fatigue, facial/lower extremity edema, nausea and vomiting, diarrhea, generalized rash, and new-onset proteinuria. Treatment with imatinib showed a trend toward improvement in the FVC % predicted (1.74%; P not significant) and the MRSS (3.9 units; P < 0.001). Use of high-dose daily therapy with imatinib (600 mg/day) in SSc patients with ILD was associated with a large number of AEs. Our experience with AEs suggests that dosages of imatinib lower than 600 mg/day may be appropriate and that further dose ranging analysis is needed in order to understand the therapeutic index of imatinib in SSc.", "Interstitial lung disease in systemic sclerosis (SSc-ILD) is a major cause of SSc-related death. Imunosuppressive treatment (IS) is used in patients with SSc for various organ manifestations mainly to ameliorate progression of SSc-ILD. Data on everyday IS prescription patterns and clinical courses of lung function during and after therapy are scarce. We analysed patients fulfilling American College of Rheumatology (ACR)/European League against Rheumatism (EULAR) 2013 criteria for SSc-ILD and at least one report of IS. Types of IS, pulmonary function tests (PFT) and PFT courses during IS treatment were evaluated. EUSTAR contains 3778/11,496 patients with SSc-ILD (33%), with IS in 2681/3,778 (71%). Glucocorticoid (GC) monotherapy was prescribed in 30.6% patients with GC combinations plus cyclophosphamide (CYC) (11.9%), azathioprine (AZA) (9.2%), methotrexate (MTX) (8.7%), or mycophenolate mofetil (MMF) (7.3%). Intensive IS (MMF + GC, CYC or CYC + GC) was started in patients with the worst PFTs and ground glass opacifications on imaging. Patients without IS showed slightly less worsening in forced vital capacity (FVC) when starting with FVC 50-75% or >75%. GC showed negative trends when starting with FVC <50%. Regarding diffusing capacity for carbon monoxide (DLCO), negative DLCO trends were found in patients with MMF. IS is broadly prescribed in SSc-ILD. Clusters of clinical and functional characteristics guide individualised treatment. Data favour distinguished decision-making, pointing to either watchful waiting and close monitoring in the early stages or start of immunosuppressive treatment in moderately impaired lung function. Advantages of specific IS are difficult to depict due to confounding by indication. Data do not support liberal use of GC in SSc-ILD.", "The aim of this study was to evaluate efficacy of azathioprine (AZA) and cyclophosphamide (CYC) as a therapeutic regimen for interstitial lung disease associated with systemic sclerosis (SSc). Thirty-six selected patients included in this retrospective cohort and received one of the two drugs; the first group consists of 15 patients who were treated with AZA (1.5-2 mg/kg/day) and the second group with 21 patients received oral CYC (up to 2 mg/kg/day). Both groups received additional low dose of prednisolone (≤10 mg) for 6 months. Forced vital capacity (FVC), diffusion lung capacity for carbon monoxide (DLCO) and skin score were assessed as outcome measures. Modified Rodnan skin score (mRSS), pulmonary function test and DLCO were evaluated at entry and at the end of study after 12 months. The mean (SD) FVC percentages obtained at baseline and post-treatment in AZA-treated patients were 62.8 ± 9.8 and 71.1 ± 20.9 with mean difference of FVC% +7.6 ± 13.1, p = 0.05, and in CYC-treated patients 59.5 ± 10.7, 63.1 ± 16.2 and +2.9 ± 11.5, respectively, p = 0.19. Baseline and post-treatment DLCO% in AZA-treated patients were 61.4 ± 25.8 and 76.7 ± 24.0 with mean difference of +15.0 ± 14.5, respectively, p = 0.01. In CYC-treated patients, those measures were 67.7 ± 27.5 and 60.0 ± 22.9 with mean difference of -8.0 ± 23.7 (p = 0.12). Following 12 months of treatment in AZA-treated patients, mean difference of changes in mRSS was -2.9 ± 3.7 and -1.4 ± 4.5 in CYC-treated patients. Our results indicated that AZA can be effective in ameliorating or stabilizing lung function in selected SSc patient groups.", "Systemic sclerosis is a heterogeneous disease of unknown etiology with limited effective therapies. It is characterized by autoimmunity, vasculopathy, and fibrosis and is clinically manifested by multiorgan involvement. Interstitial lung disease is a common complication of systemic sclerosis and is associated with significant morbidity and mortality. The diagnosis of interstitial lung disease hinges on careful clinical evaluation and pulmonary function tests and high-resolution computed tomography. Effective therapeutic options are still limited. Several experimental therapies are currently in early-phase clinical trials and show promise.", "A unique feature of systemic sclerosis (SSc) that distinguishes it from other fibrotic disorders is that autoimmunity and vasculopathy characteristically precede fibrosis. Moreover, fibrosis in SSc is not restricted to a single organ, but rather affects many organs and accounts for much of the morbidity and mortality associated with this disease. Although immunomodulatory drugs have been used extensively in the treatment of SSc, no therapy to date has been able to reverse or slow the progression of tissue fibrosis or substantially modify the natural progression of the disease. In this Review, we highlight recent studies that shed light on the cellular and molecular mechanisms underlying the fibrotic process in SSc and that identify cellular processes and intra- and extracellular proteins as potential novel targets for therapy in this prototypic multisystemic fibrotic disease." ]
Identification of Fine Epitopes on the N- and C- Terminals of Nucleocapsid Protein from Crimean-Congo Hemorrhagic Fever Virus	Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne pathogen that causes severe disease in humans. CCHFV is widely distributed in more than 30 countries and distinct regions, which means that it poses a serious threat to human health. The nucleocapsid protein (NP) encoded by the CCHFV S gene is the primary detectable antigen in infected cells, which makes it an important viral antigen and a clinical diagnostic target. In this study, the modified biosynthetic peptide (BSP) method was used to identify the fine epitopes on the N- and C- terminals of NP from the CCHFV YL04057 strain using rabbit antiserum against CCHFV-NP. Nine epitopes were identified: E1a (178NLILNRGG185), E1b (184GGDENP189), E2 (352PLKWGKK358), E3 (363FADDS367), E4 (399NPDDAA404), E5a (447DIVASEHL454), E5b (452EHLLHQSL459), E6 (464SPFQNAY470) and E7 (475NATSANII482). Western blotting analysis showed that each epitope interacted with the positive serum of sheep that had been naturally infected with CCHFV. Amino acid sequence alignment between each epitope and their homologous proteins showed that they were almost 100% conserved among 12 CCHFV sequences from different lineages, except for epitopes E1a, E1b and E2. Three-dimensional structural modeling analysis showed that all identified epitopes were located on the surface of the NP "head" domain. This study identified fine epitopes on the N- and C- terminals of NP, which will increase the understanding of the structure and function of NP, and it could lay the foundation for the design and development of a CCHFV multi-epitope peptide vaccine and detection antigen.	[ "Crimean-Congo hemorrhagic fever virus (genus Nairovirus, family Bunyaviridae) genome M segment encodes an unusually large (in comparison to members of other genera) polyprotein (1,684 amino acids in length) containing the two major structural glycoproteins, Gn and Gc, that are posttranslationally processed from precursors PreGn and PreGc by SKI-1 and SKI-1-like proteases, respectively. The characteristics of the N-terminal 519 amino acids located upstream of the mature Gn are unknown. A highly conserved furin/proprotein convertase (PC) cleavage site motif (RSKR247) is located between the variable N-terminal region that is predicted to have mucin-like properties and the rest of PreGn. Mutational analysis of the RSKR247 motif and use of a specific furin/PC inhibitor and brefeldin A demonstrate that furin/PC cleavage occurs at the RSKR247 motif of PreGn as the protein transits the trans Golgi network and generates a novel glycoprotein designated GP38. Immunoprecipitation analysis identified two additional proteins, GP85 and GP160, which contain both mucin and GP38 domain regions, and whose generation does not involve furin/PC cleavage. Consistent with glycosylation predictions, heavy O-linked glycosylation and moderate levels of N-glycans were detected in the GP85 and GP160 proteins, both of which contain the mucin domain. GP38, GP85, and GP160 are likely soluble proteins based on the lack of predicted transmembrane domains, their detection in virus-infected cell supernatants, and the apparent absence from virions. Analogy with soluble glycoproteins and mucin-like proteins encoded by other hemorrhagic fever-associated RNA viruses suggests these proteins could play an important role in viral pathogenesis.", "Glycans are key molecules in many physiological and pathological processes. As with other molecules, like proteins, visualization of the 3D structures of glycans adds valuable information for understanding their biological function. Hence, here we introduce Azahar, a computing environment for the creation, visualization and analysis of glycan molecules. Azahar is implemented in Python and works as a plugin for the well known PyMOL package (Schrodinger in The PyMOL molecular graphics system, version 1.3r1, 2010). Besides the already available visualization and analysis options provided by PyMOL, Azahar includes 3 cartoon-like representations and tools for 3D structure caracterization such as a comformational search using a Monte Carlo with minimization routine and also tools to analyse single glycans or trajectories/ensembles including the calculation of radius of gyration, Ramachandran plots and hydrogen bonds. Azahar is freely available to download from http://www.pymolwiki.org/index.php/Azahar and the source code is available at https://github.com/agustinaarroyuelo/Azahar .", "The complete nucleotide sequences of the medium (M) segment of seven Chinese isolates of Crimean-Congo hemorrhagic fever (CCHF) virus were determined. The M-segment RNA of CCHF virus comprises 5356-5377 nucleotides depending on the isolate and encodes a protein comprising 1689-1697 amino acids in a viral complementary sense. Phylogenetic analysis of the M segment showed that the Chinese CCHF virus isolates were clustered into three groups, one of which was more closely related to a Nigerian isolate. Pairwise comparison of a precursor protein showed that amino-terminal regions comprising 250 amino acids were extraordinary heterogeneous, with a 22.4% identity in amino acids being observed between the most distantly related isolates. Since all the viruses were isolated from 1966 to 1988 within a restricted area in the Xinjiang Autonomous Region in western China, the results indicate that a multisource virus population is endemic in this region.", "Crimean-Congo hemorrhagic fever (CCHF) is a severe illness with high case fatality that occurs in Africa, Europe, the Middle East, and Asia. The complete genomes of 13 geographically and temporally diverse virus strains were determined, and CCHF viruses were found to be highly variable with 20 and 8%, 31 and 27%, and 22 and 10% nucleotide and deduced amino acid differences detected among virus S (nucleocapsid), M (glycoprotein), and L (polymerase) genome segments, respectively. Distinct geographic lineages exist, but with multiple exceptions indicative of long-distance virus movement. Discrepancies among the virus S, M, and L phylogenetic tree topologies document multiple RNA segment reassortment events. An analysis of individual segment datasets suggests genetic recombination also occurs. For an arthropod-borne virus, the genomic plasticity of CCHF virus is surprisingly high.", "In Senegal, wild ground-feeding birds are frequently infested with immature ticks. In two areas where numerous Crimean-Congo haemorrhagic fever (CCHF) virus isolations were obtained from Hyalomma marginatum rufipes adult ticks collected on ungulates, 175 birds were captured and sera collected. CCHF antibodies were detected by ELISA in 6/22 red-beaked hornbills (Tockus erythrorhynchus), 2/11 glossy starlings (Lamprotornis sp.) and 1/3 guinea fowls. The virus was isolated from H. m. rufipes nymphs collected on a hornbill. The role of wild ground-feeding birds in CCHF virus ecology in West Africa is discussed.", "Crimean-Congo hemorrhagic fever virus (CCHFV) is an emerging tick-borne virus of the Bunyaviridae family that is responsible for a fatal human disease for which preventative or therapeutic measures do not exist. We solved the crystal structure of the CCHFV strain Baghdad-12 nucleocapsid protein (N), a potential therapeutic target, at a resolution of 2.1 Å. N comprises a large globular domain composed of both N- and C-terminal sequences, likely involved in RNA binding, and a protruding arm domain with a conserved DEVD caspase-3 cleavage site at its apex. Alignment of our structure with that of the recently reported N protein from strain YL04057 shows a close correspondence of all folds but significant transposition of the arm through a rotation of 180 degrees and a translation of 40 Å. These observations suggest a structural flexibility that may provide the basis for switching between alternative N protein conformations during important functions such as RNA binding and oligomerization. Our structure reveals surfaces likely involved in RNA binding and oligomerization, and functionally critical residues within these domains were identified using a minigenome system able to recapitulate CCHFV-specific RNA synthesis in cells. Caspase-3 cleaves the polypeptide chain at the exposed DEVD motif; however, the cleaved N protein remains an intact unit, likely due to the intimate association of N- and C-terminal fragments in the globular domain. Structural alignment with existing N proteins reveals that the closest CCHFV relative is not another bunyavirus but the arenavirus Lassa virus instead, suggesting that current segmented negative-strand RNA virus taxonomy may need revision.", "Arthropod-borne viruses (arboviruses) generally require horizontal transmission by arthropod vectors among vertebrate hosts for their natural maintenance. This requirement for alternate replication in disparate hosts places unusual evolutionary constraints on these viruses, which have probably limited the evolution of arboviruses to only a few families of RNA viruses (Togaviridae, Flaviviridae, Bunyaviridae, Rhabdoviridae, Reoviridae, and Orthomyxoviridae) and a single DNA virus. Phylogenetic studies have suggested the dominance of purifying selection in the evolution of arboviruses, consistent with constraints imposed by differing replication environments and requirements in arthropod and vertebrate hosts. Molecular genetic studies of alphaviruses and flaviviruses have also identified several mutations that effect differentially the replication in vertebrate and mosquito cells, consistent with the view that arboviruses must adopt compromise fitness characteristics for each host. More recently, evidence of positive selection has also been obtained from these studies. However, experimental model systems employing arthropod and vertebrate cell cultures have yielded conflicting conclusions on the effect of alternating host infections, with host specialization inconsistently resulting in fitness gains or losses in the bypassed host cells. Further studies using in vivo systems to study experimental arbovirus evolution are critical to understanding and predicting disease emergence, which often results from virus adaptation to new vectors or amplification hosts. Reverse genetic technologies that are now available for most arbovirus groups should be exploited to test assumptions and hypotheses derived from retrospective phylogenetic approaches.", "Crimean-Congo hemorrhagic fever (CCHF) virus is the cause of an important tick-borne disease of humans throughout regions of Africa, Europe, and Asia. Like other members of the genus Nairovirus, family Bunyaviridae, the CCHF virus M genome RNA segment encodes the virus glycoproteins. Sequence analysis of the CCHF virus (Matin strain) M RNA segment revealed one major open reading frame that potentially encodes a precursor polyprotein 1,689 amino acids (aa) in length. Comparison of the deduced amino acid sequences of the M-encoded polyproteins of Nigerian, Pakistani, and Chinese CCHF virus strains revealed two distinct protein regions. The carboxyl-terminal 1,441 aa are relatively highly conserved (up to 8.4% identity difference), whereas the amino-terminal 243 to 248 aa are highly variable (up to 56.4% identity difference) and have mucin-like features, including a high serine, threonine, and proline content (up to 47.3%) and a potential for extensive O-glycosylation. Analysis of released virus revealed two major structural glycoproteins, G2 (37 kDa) and G1 (75 kDa). Virus protein analysis by various techniques, including pulse-chase analysis and/or reactivity with CCHF virus-specific polyclonal and antipeptide antibodies, demonstrated that the 140-kDa (which contains the mucin-like region) and 85-kDa nonstructural proteins are the precursors of the mature G2 and G1 proteins, respectively. The amino termini of the CCHF virus (Matin strain) G2 and G1 proteins were established by microsequencing to be equivalent to aa 525 and 1046, respectively, of the encoded polyprotein precursor. The tetrapeptides RRLL and RKPL are immediately upstream of the cleavage site for mature G2 and G1, respectively. These are completely conserved among the predicted polyprotein sequences of all the CCHF virus strains and closely resemble the tetrapeptides that represent the major cleavage recognition sites present in the glycoprotein precursors of arenaviruses, such as Lassa fever virus (RRLL) and Pichinde virus (RKLL). These results strongly suggest that CCHF viruses (and other members of the genus Nairovirus) likely utilize the subtilase SKI-1/S1P-like cellular proteases for the major glycoprotein precursor cleavage events, as has recently been demonstrated for the arenaviruses." ]
Long-term survival and antibiotic tolerance in Pseudomonas aeruginosa incubated in water	Pseudomonas aeruginosa is capable of long-term survival in water, which may serve as a reservoir for infection. Although viable cell counts of PAO1 incubated in water remain stable throughout 8 weeks, LIVE/DEAD staining indicated a high proportion of cells stained with propidium iodide (PI). The proportion of PI-stained cells increased by 4 weeks, then decreased again by 8 weeks, suggesting an adaptive response. This was also evident in an observed shift in cell morphology from a rod to a coccoid shape after 8 weeks. Fluorescence-activated cell sorting (FACS) was used to recover PI-stained cells, which were plated and shown to be viable, indicating that PI-stained cells were membrane-compromised but still cultivable. PAO1 mid-log cells in water were labeled with the dsDNA-binding dye PicoGreen to monitor viability as well as DNA integrity, which demonstrated that the population remains viable and transitions towards increased dsDNA staining. Metabolic activity was found to decrease significantly in water by 4 weeks. The PAO1 outer membrane became less permeable and more resistant to polymyxin B damage in water, and the profile of total membrane lipids changed over time. Among the ~1400 transcriptional lux fusions, gene expression in water revealed that the majority of genes were repressed, but subsets of genes were induced at particular time points. In summary, these results indicate that P. aeruginosa is dormant in water and this adaptation involves a complex pattern of gene regulation and changes to the cell to promote long-term survival and antibiotic tolerance. The approach of P. aeruginosa incubated in water may be useful to study antibiotic tolerance and the mechanisms of dormancy and survival in nutrient limiting conditions.	[ "A specific high affinity galactose transport system called P(betag) can be induced by trace amounts of galactose in the medium by virtue of its own ability to capture and accumulate galactose. The transport system is coregulated with the production of a high affinity periplasmic galactose binding protein, which constitutes but one part of the transport system. Some transport negative mutants still remain producers of this binding protein. A close correlation exists between production of the active binding protein and the presence of galactose chemotaxis. The hypothesis, that this binding protein is a common element of the specific galactose transport system, P(betag), and of galactose chemotaxis is supported by observations on structural mutants, being defective in galactose binding protein as well as showing a lack of galactose chemotaxis. The binding protein is a monomer with two binding sites for galactose. Binding of one or two of the galactose molecules elicits specific conformational changes of the galactose binding protein (lowered affinity for galactose, increase of charges of the protein, increased fluorescence of tryptophan residues). The importance of these features for transport and for chemotaxis is discussed (70).", "The cells of the marine bacterium Ant-300 were found to take up arginine when this substrate was at low concentrations. The cells possessed an uptake system(s) that specifically transported l-arginine. The kinetic parameters for uptake appeared to differ when the cells were exposed to nanomolar and micromolar concentrations of the amino acid. Uptake over this concentration range functioned in the absence of an exogenous energy source, even after the cells had been preincubated in unsupplemented artificial seawater. Respiratory activity appeared to be a more important driving force for arginine uptake than adenosine 5'-triphosphate hydrolysis. The cells also exhibited chemotaxis toward l-arginine. The minimum arginine concentration needed to elicit a chemotactic response was between 10 and 10 M. It is proposed that the capture of arginine by cells of Ant-300 in nutrient-depleted waters, which are typical of the open ocean, proceeds via high-affinity active transport, whereas in substrate-enriched seawater, capture involves chemotaxis and an active transport mechanism with reduced affinity for the substrate." ]
Role of retinoic acid in lung epithelial progenitor cells	Despite compelling data describing pro-regenerative effects of all-trans retinoic acid (ATRA) in pre-clinical models of chronic obstructive pulmonary disease (COPD), clinical trials using retinoids for emphysema patients have failed. Crucial information about the specific role of RA signaling in adult rodent and human lung epithelial progenitor cells is largely missing.	[ "The conducting airways (bronchi and bronchioles) and peripheral gas exchange (alveolar) regions of the mammalian lung are generated by a process of branching morphogenesis. Evidence suggests that during embryonic development, the undifferentiated epithelial progenitors are located at the distal tips of the branching epithelium. To test this hypothesis, we used an Id2-CreER(T2) knock-in mouse strain to lineage trace the distal epithelial tip cells during either the pseudoglandular or canalicular phases of development. During the pseudoglandular stage, the tip cells both self-renew and contribute descendents to all epithelial cell lineages, including neuroendocrine cells. In addition, individual Id2(+) tip cells can self-renew and contribute descendents to both the bronchiolar and alveolar compartments. By contrast, during the later canalicular stage, the distal epithelial tip cells only contribute descendents to the alveoli. Taken together, this evidence supports a model in which the distal tip of the developing lung contains a multipotent epithelial population, the fate of which changes during development.", "The role of lung epithelial stem cells in maintenance and repair of the adult lung is ill-defined, and their identity remains contentious because of the lack of definitive markers for their prospective isolation and the absence of clonogenic assays able to measure their stem/progenitor cell potential. In this study, we show that replication of epithelial-mesenchymal interactions in a previously undescribed matrigel-based clonogenic assay enables the identification of lung epithelial stem/progenitor cells by their colony-forming potential in vitro. We describe a population of EpCAM(hi) CD49f(pos) CD104(pos) CD24(low) epithelial cfus that generate colonies comprising airway, alveolar, or mixed lung epithelial cell lineages when cocultured with EpCAM(neg) Sca-1(pos) lung mesenchymal cells. We show that soluble fibroblast growth factor-10 and hepatocyte growth factor partially replace the requirement for mesenchymal support of epithelial colony formation, allowing clonal passaging and demonstration of their capacity for self-renewal. These data support a model in which the adult mouse lung contains a minor population of multipotent epithelial stem/progenitor cells with the capacity for self-renewal and whose descendants give rise to airway and alveolar epithelial cell lineages in vitro.", "Herein, we have identified cross-talk between the Hippo and fibroblast growth factor receptor (FGFR) oncogenic signaling pathways in cholangiocarcinoma (CCA). Yes-associated protein (YAP) nuclear localization and up-regulation of canonical target genes was observed in CCA cell lines and a patient-derived xenograft (PDX). Expression of FGFR1, -2, and -4 was identified in human CCA cell lines, driven, in part, by YAP coactivation of TBX5. In turn, FGFR signaling in a cell line with minimal basal YAP expression induced its cellular protein expression and nuclear localization. Treatment of YAP-positive CCA cell lines with BGJ398, a pan-FGFR inhibitor, resulted in a decrease in YAP activation. FGFR activation of YAP appears to be driven largely by FGF5 activation of FGFR2, as siRNA silencing of this ligand or receptor, respectively, inhibited YAP nuclear localization. BGJ398 treatment of YAP-expressing cells induced cell death due to Mcl-1 depletion. In a YAP-associated mouse model of CCA, expression of FGFR 1, 2, and 4 was also significantly increased. Accordingly, BGJ398 treatment was tumor-suppressive in this model and in a YAP-positive PDX model. These preclinical data suggest not only that the YAP and Hippo signaling pathways culminate in an Mcl-1-regulated tumor survival pathway but also that nuclear YAP expression may be a biomarker to employ in FGFR-directed therapy.", "Our understanding of how stem cells are regulated to maintain appropriate tissue size and architecture is incomplete. We show that Yap (Yes-associated protein 1) is required for the actual maintenance of an adult mammalian stem cell. Without Yap, adult airway basal stem cells are lost through their unrestrained differentiation, resulting in the simplification of a pseudostratified epithelium into a columnar one. Conversely, Yap overexpression increases stem cell self-renewal and blocks terminal differentiation, resulting in epithelial hyperplasia and stratification. Yap overexpression in differentiated secretory cells causes them to partially reprogram and adopt a stem cell-like identity. In contrast, Yap knockdown prevents the dedifferentiation of secretory cells into stem cells. We then show that Yap functionally interacts with p63, the cardinal transcription factor associated with myriad epithelial basal stem cells. In aggregate, we show that Yap regulates all of the cardinal behaviors of airway epithelial stem cells and determines epithelial architecture.", "One of the three human retinoic acid receptors, RAR-beta, maps to a region on the short arm of chromosome 3 frequently deleted in lung cancer. Because retinoic acid is required for normal epithelial cell growth and regulation, and loss of a retinoic acid receptor might be expected to contribute to oncogenesis, we examined RAR-beta RNA and DNA in normal lung, 33 lung cancer cell lines and nine primary lung tumors. Normally, RAR-beta is expressed as two transcripts, of sizes 3.1 kb and 2.8 kb, which are strongly induced by retinoic acid. At least 50% of the cell lines and 30% of the tumor samples show altered RAR-beta expression and/or inducibility, including examples of absence or specific loss of one of the RAR-beta transcripts. Abnormalities in the expression patterns of RAR-alpha and RAR-gamma also are found, but at a lower frequency than RAR-beta abnormalities. Southern analysis reveals alteration of the RAR-beta gene in three of the cell lines. Our data suggest that abnormalities in structure and expression of the RAR-beta gene may be involved in the pathogenesis of lung cancer.", "The use of retinoids to induce human lung regeneration is under investigation in a number of studies in patients with chronic obstructive pulmonary disease (COPD). Retinoic acid (RA) has complex pleiotropic functions during vertebrate patterning and development and can induce regeneration in a number of different organ systems. Studies of retinoid signalling during lung development might provide a molecular basis to explain pharmacological induction of alveolar regeneration in adult models of lung disease. In this review the role of endogenous RA signalling during alveologenesis is explored and data suggesting that a number of exogenous retinoids can induce regeneration in the adult lung are discussed. Current controversies in this area are highlighted and a hypothesis of lung regeneration is put forward. Understanding the cellular and molecular mechanisms of induction of regeneration will be central for effective translation into patients with lung disease and may reveal novel insights into the pathogenesis of alveolar disease and senescence.", "This Executive Summary of the Global Strategy for the Diagnosis, Management, and Prevention of COPD, Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2017 report focuses primarily on the revised and novel parts of the document. The most significant changes include: (1) the assessment of chronic obstructive pulmonary disease has been refined to separate the spirometric assessment from symptom evaluation. ABCD groups are now proposed to be derived exclusively from patient symptoms and their history of exacerbations; (2) for each of the groups A to D, escalation strategies for pharmacologic treatments are proposed; (3) the concept of deescalation of therapy is introduced in the treatment assessment scheme; (4) nonpharmacologic therapies are comprehensively presented; and (5) the importance of comorbid conditions in managing chronic obstructive pulmonary disease is reviewed.", "Palovarotene is an oral γ-selective retinoid agonist. In animal emphysema models, palovarotene reduced inflammation, promoted structural repair and functional improvement. REPAIR (Retinoid treatment of Emphysema in Patients on the α(1)-antitrypsin International Registry), was an investigator-initiated, double-blind, placebo-controlled randomised study to assess the safety and efficacy of 5 mg·day(-1) palovarotene given for 1 year to 262 patients with severe α(1)-antitrypsin deficiency and emphysema confirmed by computed tomography. Change in volume-adjusted 15th percentile point lung density from baseline in 1 year was the primary end-point; functional end-points were also regularly assessed. We randomly assigned 133 and 129 patients to placebo or palovarotene, respectively. Both groups were well matched for all baseline characteristics, including respiratory medications. 88% and 85% of patients completed 1 year of treatment with placebo and palovarotene, respectively. Palovarotene was generally well tolerated. In the study completers population, the placebo-corrected difference of lung density was -0.45 HU at week 28 (p=0.64) and -0.25 HU at week 52 (p=0.94). A nonsignificant treatment difference in most functional parameters of the lung in favour of the drug was observed over time suggesting potential pharmacological effects of palovarotene. Palovarotene 5 mg·day(-1) over 1 yr failed to show a significant benefit on lung density in moderate-to-severe emphysema secondary to severe α(1)-antitrypsin deficiency.", "Retinoids, analogues of vitamin A, are required for the normal growth and differentiation of human bronchial epithelium. They are also able to reverse premalignant lesions and prevent second primary tumors in some patients with non-small-cell lung cancer (NSCLC). These effects are thought to result from modulation of cell growth, differentiation, or apoptosis (programmed cell death). When certain retinoid receptors in the cell nucleus (i.e., retinoic acid receptors [RARs] and retinoid X receptors [RXRs]), which mediate most retinoid actions, are suppressed, abnormal activity may result that could enhance cancer development. This study was designed to determine whether there are abnormalities in the expression of retinoid receptors in surgical specimens from patients with NSCLC. Transcripts of nuclear retinoid receptors were detected in formalin-fixed, paraffin-embedded specimens by use of digoxigenin-labeled riboprobes specific for RAR alpha, RAR beta, RAR gamma, RXR alpha, RXR beta, and RXR gamma for in situ hybridization to histologic specimens from 79 patients with NSCLC and as control from 17 patients with non-lung cancer. The quality and specificity of the digoxigenin-labeled probes were determined by northern blotting, and the specificity of the binding of antisense riboprobes was verified by use of sense probes as controls. All receptors were expressed in at least 89% of control normal bronchial tissue specimens from 17 patients without a primary lung cancer and in distant normal bronchus specimens from patients with NSCLC. RAR alpha, RXR alpha, and RXR gamma were expressed in more than 95% of the NSCLC specimens. In contrast, RAR beta, RAR gamma, and RXR beta expression was detected in only 42%, 72%, and 76% of NSCLC, respectively. These data suggest that the expression of RAR alpha, RXR alpha, and RXR gamma is not altered in NSCLC; however, expression of RAR beta and possibly also of RAR gamma and RXR beta is suppressed in a large percentage of patients with lung cancer. The loss of expression of one or more of these nuclear retinoid receptors may be associated with lung carcinogenesis." ]
Deep learning-based quantification of visceral and subcutaneous fat in congenic mice	Obesity is increasingly prevalent and associated with increased risk of developing type 2 diabetes, cardiovascular diseases, and cancer. Magnetic resonance imaging (MRI) is an accurate method for determination of body fat volume and distribution. However, quantifying body fat from numerous MRI slices is tedious and time-consuming. Here we developed a deep learning-based method for measuring visceral and subcutaneous fat in the abdominal region of mice. Congenic mice only differ from C57BL/6 (B6) Apoe knockout (Apoe-/-) mice in chromosome 9 that is replaced by C3H/HeJ genome. Male congenic mice had lighter body weight than B6-Apoe-/- mice after being fed 14 weeks of Western diet. Axial and coronal T1-weighted sequencing at 1-mm-thickness and 1-mm-gap was acquired with a 7T Bruker ClinScan scanner. A deep learning approach was developed for segmenting visceral and subcutaneous fat based on the U-net architecture made publicly available through the open-source ANTsRNet library-a growing repository of well-known neural networks. The volumes of subcutaneous and visceral fat measured through our approach were highly comparable with those from manual measurements. The Dice score, root-mean-square error (RMSE), and correlation analysis demonstrated the similarity between two methods in quantifying visceral and subcutaneous fat. Analysis with the automated method showed significant reductions in volumes of visceral and subcutaneous fat but not non-fat tissues in congenic mice compared to B6 mice. These results demonstrate the accuracy of deep learning in quantification of abdominal fat and its significance in determining body weight.	[ "Inbred mouse strains C57BL/6J (B6) and C3H/HeJ (C3H) differ significantly in atherosclerosis susceptibility and plasma lipid levels on the apolipoprotein E-deficient (apoE-/-) background when fed a Western diet. To determine genetic factors contributing to the variations in these phenotypes, we performed quantitative trait locus (QTL) analysis using an intercross between the two strains carrying the apoE-/- gene. Atherosclerotic lesions at the aortic root and plasma lipid levels of 234 female F2 mice were analyzed after being fed a Western diet for 12 weeks. QTL analysis revealed one significant QTL, named Ath22 (42 cM, LOD 4.1), on chromosome 9 and a suggestive QTL near D11mit236 (20 cM, LOD 2.4) on chromosome 11 that influenced atherosclerotic lesion size. One significant QTL on distal chromosome 1, which accounted for major variations in plasma LDL/VLDL cholesterol and triglyceride levels, coincided with a QTL having strong effects on body weight. Plasma LDL/VLDL cholesterol or triglyceride levels of F2 mice were significantly correlated with body weight, but they were not correlated with atherosclerotic lesion sizes. These data indicate that atherosclerosis susceptibility and plasma cholesterol levels are controlled by separate genetic factors in the B6 and C3H mouse model and that genetic linkages exist between body weight and lipoprotein metabolism.", "Biologists can now prepare and image thousands of samples per day using automation, enabling chemical screens and functional genomics (for example, using RNA interference). Here we describe the first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).", "Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.", "Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks. Concise overviews are provided of studies per application area: neuro, retinal, pulmonary, digital pathology, breast, cardiac, abdominal, musculoskeletal. We end with a summary of the current state-of-the-art, a critical discussion of open challenges and directions for future research.", "Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections. We developed a fully automatic, non-rigid but as-rigid-as-possible registration method for large tiled serial section microscopy stacks. We use the Scale Invariant Feature Transform (SIFT) to identify corresponding landmarks within and across sections and globally optimize the pose of all tiles in terms of least square displacement of these landmark correspondences. We evaluate the precision of the approach using an artificially generated dataset designed to mimic the properties of TEM data. We demonstrate the performance of our method by registering an ssTEM dataset of the first instar larval brain of Drosophila melanogaster consisting of 6885 images. This method is implemented as part of the open source software TrakEM2 (http://www.ini.uzh.ch/~acardona/trakem2.html) and distributed through the Fiji project (http://pacific.mpi-cbg.de).", "Gleason grading of histological images is important in risk assessment and treatment planning for prostate cancer patients. Much research has been done in classifying small homogeneous cancer regions within histological images. However, semi-supervised methods published to date depend on pre-selected regions and cannot be easily extended to an image of heterogeneous tissue composition. In this paper, we propose a multi-scale U-Net model to classify images at the pixel-level using 224 histological image tiles from radical prostatectomies of 20 patients. Our model was evaluated by a patient-based 10-fold cross validation, and achieved a mean Jaccard index of 65.8% across 4 classes (stroma, Gleason 3, Gleason 4 and benign glands), and 75.5% for 3 classes (stroma, benign glands, prostate cancer), outperforming other methods.", "To adapt the so-called nonlocal means filter to deal with magnetic resonance (MR) images with spatially varying noise levels (for both Gaussian and Rician distributed noise). Most filtering techniques assume an equal noise distribution across the image. When this assumption is not met, the resulting filtering becomes suboptimal. This is the case of MR images with spatially varying noise levels, such as those obtained by parallel imaging (sensitivity-encoded), intensity inhomogeneity-corrected images, or surface coil-based acquisitions. We propose a new method where information regarding the local image noise level is used to adjust the amount of denoising strength of the filter. Such information is automatically obtained from the images using a new local noise estimation method. The proposed method was validated and compared with the standard nonlocal means filter on simulated and real MRI data showing an improved performance in all cases. The new noise-adaptive method was demonstrated to outperform the standard filter when spatially varying noise is present in the images." ]
BRD8 is involved in p53-dependent gene suppression and DNA damage repair	Regulation of the chromatin state is crucial for biological processes such as the regulation of transcription, DNA replication, and DNA damage repair. Here we show that knockdown of the BRD8 bromodomain protein - a subunit of the p400/Tip60 complex - leads to p21 induction, and concomitant cell cycle arrest in G1/S. We further demonstrate that the p53 transcriptional pathway is activated in BRD8-depleted cells, and this accounts for upregulation of not only p21 but also of pro-apoptotic genes, leading to subsequent apoptosis. Importantly, the DNA damage response (DDR) is induced upon BRD8 depletion, and DNA damage foci are detectable in BRD8-depleted cells under normal growth conditions. Consistently with an activated DDR, we find that in BRD8-depleted cells, the ATM-CHK2 DDR pathway is turned on but, CHK1 proteins levels are severely reduced and replication stress is detectable as enhanced replication protein A (RPA32) phosphorylation levels. Notably, acetylation of histone H4 at K16 (H4K16ac) is reduced in BRD8-depleted cells, suggesting that BRD8 may have a role in the recruitment and/or stabilization of the p400/Tip60 complex within chromatin, thereby facilitating DNA repair. Taken together, our results suggest that BRD8 is involved not only in p53-dependent gene suppression, but also in the maintenance of genome stability.	[ "The serine/threonine protein kinase ATM signals to cell cycle and DNA repair components by phosphorylating downstream targets such as p53, CHK2, NBS1, and BRCA1. Mutation of ATM occurs in the human autosomal recessive disorder ataxia-telangiectasia, which is characterized by hypersensitivity to ionizing radiation and a failure of cells to arrest the cell cycle after the induction of DNA double-strand breaks. It has thus been proposed that ATM inhibition would cause cellular radio- and chemosensitization. Through screening a small molecule compound library developed for the phosphatidylinositol 3'-kinase-like kinase family, we identified an ATP-competitive inhibitor, 2-morpholin-4-yl-6-thianthren-1-yl-pyran-4-one (KU-55933), that inhibits ATM with an IC(50) of 13 nmol/L and a Ki of 2.2 nmol/L. KU-55933 shows specificity with respect to inhibition of other phosphatidylinositol 3'-kinase-like kinases. Cellular inhibition of ATM by KU-55933 was demonstrated by the ablation of ionizing radiation-dependent phosphorylation of a range of ATM targets, including p53, gammaH2AX, NBS1, and SMC1. KU-55933 did not show inhibition of UV light DNA damage induced cellular phosphorylation events. Exposure of cells to KU-55933 resulted in a significant sensitization to the cytotoxic effects of ionizing radiation and to the DNA double-strand break-inducing chemotherapeutic agents, etoposide, doxorubicin, and camptothecin. Inhibition of ATM by KU-55933 also caused a loss of ionizing radiation-induced cell cycle arrest. By contrast, KU-55933 did not potentiate the cytotoxic effects of ionizing radiation on ataxia-telangiectasia cells, nor did it affect their cell cycle profile after DNA damage. We conclude that KU-55933 is a novel, specific, and potent inhibitor of the ATM kinase.", "The ataxia telangiectasia mutant (ATM) protein kinase regulates the cell's response to DNA damage through the phosphorylation of proteins involved in cell-cycle checkpoints and DNA repair. However, the signal-transduction pathway linking DNA strand breaks to activation of ATM's kinase activity is not clearly defined. Here, we demonstrate that DNA damage induces the rapid acetylation of ATM. This acetylation depends on the Tip60 histone acetyltransferase (HAT). Suppression of Tip60 blocks the activation of ATM's kinase activity and prevents the ATM-dependent phosphorylation of p53 and chk2. Further, inactivation of Tip60 sensitizes cells to ionizing radiation. ATM forms a stable complex with Tip60 through the conserved FATC domain of ATM. The interaction between ATM and Tip60 is not regulated in response to DNA damage. Instead, the HAT activity of the ATM-Tip60 complex is specifically activated by DNA damage. Furthermore, this activation of Tip60 by DNA damage and the recruitment of the ATM-Tip60 complex to sites of DNA damage is independent of ATM's kinase activity. The results demonstrate that the Tip60 HAT plays a key role in the activation of ATM's kinase activity in response to DNA damage.", "The complexity of chromatin architecture presents a significant barrier to the ability of the DNA repair machinery to access and repair DNA double-strand breaks (DSBs). Consequently, remodeling of the chromatin landscape adjacent to DSBs is vital for efficient DNA repair. Here, we demonstrate that DNA damage destabilizes nucleosomes within chromatin regions that correspond to the γ-H2AX domains surrounding DSBs. This nucleosome destabilization is an active process requiring the ATPase activity of the p400 SWI/SNF ATPase and histone acetylation by the Tip60 acetyltransferase. p400 is recruited to DSBs by a mechanism that is independent of ATM but requires mdc1. Further, the destabilization of nucleosomes by p400 is required for the RNF8-dependent ubiquitination of chromatin, and for the subsequent recruitment of brca1 and 53BP1 to DSBs. These results identify p400 as a novel DNA damage response protein and demonstrate that p400-mediated alterations in nucleosome and chromatin structure promote both chromatin ubiquitination and the accumulation of brca1 and 53BP1 at sites of DNA damage.", "The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. Its catalytic component, Esa1, is essential for cell cycle progression, gene-specific regulation and has been implicated in DNA repair. Almost all NuA4 subunits have clear homologues in higher eukaryotes, suggesting that the complex is conserved throughout evolution to metazoans. We demonstrate here that NuA4 complexes are indeed present in human cells. Tip60 and its splice variant Tip60b/PLIP were purified as stable HAT complexes associated with identical polypeptides, with 11 of the 12 proteins being homologs of yeast NuA4 subunits. This indicates a highly conserved subunit composition and the identified human proteins underline the role of NuA4 in the control of mammalian cell proliferation. ING3, a member of the ING family of growth regulators, links NuA4 to p53 function which we confirmed in vivo. Proteins specific to the human NuA4 complexes include ruvB-like helicases and a bromodomain-containing subunit linked to ligand-dependent transcription activation by the thyroid hormone receptor. We also demonstrate that subunits MRG15 and DMAP1 are present in distinct protein complexes harboring histone deacetylase and SWI2-related ATPase activities, respectively. Finally, analogous to yeast, a recombinant trimeric complex formed by Tip60, EPC1, and ING3 is sufficient to reconstitute robust nucleosomal HAT activity in vitro. In conclusion, the NuA4 HAT complex is highly conserved in eukaryotes, in which it plays primary roles in transcription, cellular response to DNA damage, and cell cycle control.", "We describe a protocol for creating localized DNA double-strand breaks (DSBs) with minimal requirements that can be applied in cell biology and molecular biology. This protocol is based on the combination of 5-bromo-2'-deoxyuridine (BrdU) labeling and ultraviolet C (UVC) irradiation through porous membranes. Cells are labeled with 10 μM BrdU for 48-72 h, washed with Ca(2+)- and Mg(2+)-free PBS(-), covered by polycarbonate membranes with micropores and exposed to UVC light. With this protocol, localized DSBs are created within subnuclear areas, irrespective of the cell cycle phase. Recruitment of proteins involved in DNA repair, DNA damage response, chromatin remodeling and histone modifications can be visualized without any specialized equipment. The quality is the same as that obtained by laser microirradiation or by any other focal irradiation. DSBs become visible within 30 min of UVC irradiation.", "The MRE11-RAD50-Nijmegen breakage syndrome 1 (NBS1 [MRN]) complex accumulates at sites of DNA double-strand breaks (DSBs) in microscopically discernible nuclear foci. Focus formation by the MRN complex is dependent on MDC1, a large nuclear protein that directly interacts with phosphorylated H2AX. In this study, we identified a region in MDC1 that is essential for the focal accumulation of the MRN complex at sites of DNA damage. This region contains multiple conserved acidic sequence motifs that are constitutively phosphorylated in vivo. We show that these motifs are efficiently phosphorylated by caseine kinase 2 (CK2) in vitro and directly interact with the N-terminal forkhead-associated domain of NBS1 in a phosphorylation-dependent manner. Mutation of these conserved motifs in MDC1 or depletion of CK2 by small interfering RNA disrupts the interaction between MDC1 and NBS1 and abrogates accumulation of the MRN complex at sites of DNA DSBs in vivo. Thus, our data reveal the mechanism by which MDC1 physically couples the MRN complex to damaged chromatin." ]
Incidence of Readmission in Pediatric Patients in a Tertiary Care Hospital	To determine the incidence of readmission in pediatric patients in a tertiary care hospital in a developing nation and to ascertain factors precipitating readmissions.	[ "Hospital quality measures have matured in many specialties but have lagged behind in maternity care. Recently, the National Quality Forum (NQF) has endorsed a series of 17 quality measures for perinatal care. It is important for all obstetric practitioners and leaders to understand these measures, as they form the basis of judging the quality of our hospital services for the next decade. Measure characteristics are examined including how they are developed and judged, and then the nine obstetric care measures are discussed in detail, including their literature support and specifications. The challenges of designing and testing new measures are explored. The importance of this measure set is stressed, as both the Joint Commission and the Leapfrog Group have chosen their next set of perinatal measures from this group as will state and regional public reporting organizations. Hospital quality improvement activities will be increasingly focused on improving performance on these measures. The current NQF measure set is not perfect but represents a reasonable start, covering a range of obstetric practice. Many of the measures could use further refinement and we need research and testing of additional measures going forward.", "The Seamless Transitions and (Re)admissions Network (STARNet) met in December 2012 to synthesize ongoing hospital-to-home transition work, discuss goals, and develop a plan to centralize transition information in the future. STARNet participants consisted of experts in the field of pediatric hospital medicine quality improvement and research, and included physicians and key stakeholders from hospital groups, private payers, as well as representatives from current transition collaboratives. In this report, we (1) review the current knowledge regarding hospital-to-home transitions; (2) outline the challenges of measuring and reducing readmissions; and (3) highlight research gaps and list potential measures for transition quality. STARNet met with the support of the American Academy of Pediatrics' Quality Improvement Innovation Networks and the Section on Hospital Medicine.", "To assess readmission rates identified by 3M-Potentially Preventable Readmissions software (3M-PPRs) in a national cohort of children's hospitals. A total of 1 719 617 hospitalizations for 1 531 828 unique patients in 58 children's hospitals from 2009 to 2011 from the Children's Hospital Association Case-Mix Comparative database were examined. Main outcome measures included rates, diagnoses, and costs of potentially preventable readmissions (PPRs) and all-cause readmissions. The 7-, 15-, and 30-day rates by 3M-PPRs were 2.5%, 4.1%, and 6.2%, respectively. Corresponding all-cause readmission rates were 5.0%, 8.7%, and 13.3%. At 30 days, 60.6% of all-cause readmissions were considered nonpreventable by 3M-PPRs, more than one-half of which were related to malignancies. The percentage of readmissions rated as potentially preventable was similar at all 3 time intervals. Readmissions after chemotherapy, acute leukemia, and cystic fibrosis were all considered nonpreventable, and at least 80% of readmissions after index admissions for sickle cell crisis, bronchiolitis, ventricular shunt procedures, asthma, and appendectomy were designated potentially preventable. Total costs for all readmissions were $1.7 billion; PPRs accounted for 27.3% of these costs. The most costly readmissions were associated with ventricular shunt procedures ($26.5 million/year), seizures ($15.5 million/year), and sickle cell crisis ($15.0 million/year). Rates of PPRs were significantly lower than all-cause readmission rates more than one-half of which were caused by exclusion of malignancies. Annual costs of PPRs, although significant in the aggregate, appear to represent a much smaller cost-savings opportunity for children than for adults. Our study may help guide children's hospitals to focus readmission reduction strategies on areas where the financial vulnerability is greatest based on 3M-PPRs.", "Early hospital readmission is emerging as an indicator of care quality. Some children with chronic illnesses may be readmitted on a recurrent basis, but there are limited data describing their rehospitalization patterns and impact. To describe the inpatient resource utilization, clinical characteristics, and admission reasons of patients recurrently readmitted to children's hospitals. Retrospective cohort analysis of 317,643 patients (n = 579,504 admissions) admitted to 37 US children's hospitals in 2003 with follow-up through 2008. Maximum number of readmissions experienced by each child within any 365-day interval during the 5-year follow-up period. In the sample, 69,294 patients (21.8%) experienced at least 1 readmission within 365 days of a prior admission. Within a 365-day interval, 9237 patients (2.9%) experienced 4 or more readmissions; time between admissions was a median 37 days (interquartile range [IQR], 21-63). These patients accounted for 18.8% (109,155 admissions) of all admissions and 23.2% ($3.4 billion) of total inpatient charges for the study cohort during the entire follow-up period. Tests for trend indicated that as the number of readmissions increased from 0 to 4 or more, the prevalences increased for a complex chronic condition (from 22.3% [n = 55,382/248,349] to 89.0% [n = 8225/9237]; P < .001), technology assistance (from 5.3% [n = 13,163] to 52.6% [n = 4859]; P < .001), public insurance use (from 40.9% [n = 101,575] to 56.3% [n = 5202]; P < .001), and non-Hispanic black race (from 21.8% [n = 54,140] to 34.4% [n = 3181]; P < .001); and the prevalence decreased for readmissions associated with an ambulatory care-sensitive condition (from 23.1% [62,847/272,065] to 14.0% [15,282/109,155], P < .001). Of patients readmitted 4 or more times in a 365-day interval, 2633 (28.5%) were rehospitalized for a problem in the same organ system across all admissions during the interval. Among a group of pediatric hospitals, 18.8% of admissions and 23.2% of inpatient charges were accounted for by the 2.9% of patients with frequent recurrent admissions. Many of these patients were rehospitalized recurrently for a problem in the same organ system.", "To assess variation among hospitals on pediatric readmission and revisit rates and to determine the number of high- and low-performing hospitals. In a retrospective analysis using the State Inpatient and Emergency Department Databases from the Healthcare Cost and Utilization Project with revisit linkages available, we identified pediatric (ages 1-20 years) visits with 1 of 7 common inpatient pediatric conditions (asthma, dehydration, pneumonia, appendicitis, skin infections, mood disorders, and epilepsy). For each condition, we calculated rates of all-cause readmissions and rates of revisits (readmission or presentation to the emergency department) within 30 and 60 days of discharge. We used mixed logistic models to estimate hospital-level risk-standardized 30-day revisit rates and to identify hospitals that had performance statistically different from the group mean. Thirty-day readmission rates were low (<10.0%) for all conditions. Thirty-day rates of revisit to the inpatient or emergency department setting ranged from 6.2% (appendicitis) to 11.0% (mood disorders). Study hospitals (n = 958) had low condition-specific visit volumes (37.0%-82.8% of hospitals had <25 visits). The only condition with >1% of hospitals labeled as different from the mean on 30-day risk-standardized revisit rates was mood disorders (4.2% of hospitals [n = 15], range of hospital performance 6.3%-15.9%). We found that when comparing hospitals' performances to the average, few hospitals that care for children are identified as high- or low-performers for revisits, even for common pediatric diagnoses, likely due to low hospital volumes. This limits the usefulness of condition-specific readmission or revisit measures in pediatric quality measurement.", "The purpose of this study was to characterize epidemiologic trends and cost implications of hospital readmission after treatment of pediatric appendicitis. We conducted a 5-year retrospective cohort analysis of 30-day readmission rates for 52,054 patients admitted with appendicitis at 38 children's hospitals participating in the Pediatric Health Information System database. Patients were categorized as \"uncomplicated\" (postoperative length of stay [LOS] ≤ 2 days) or \"complicated\" (LOS ≥ 3 days and ≥ 4 consecutive days of antibiotics) and analyzed for demographic data, treatment received during the index admission, readmission rates, and excess LOS and hospital-related costs attributable to readmission encounters. The aggregate 30-day readmission rate was 8.7%, and this varied significantly by disease severity and management approach (uncomplicated appendectomy, 5.6%; complicated appendectomy, 12.8%; drainage, 22.6%; antibiotics only, 24.6%; P < .0001). The median hospital cost per case attributable to readmission was $3401 (reflecting a 44% relative increase in cumulative treatment-related cost), and this varied significantly by disease severity and management approach (uncomplicated appendectomy, $1946 [31% relative increase]; complicated appendectomy, $6524 [53% increase]; drainage, $6827 [48% increase]; antibiotics only, $5835 [58% increase]; P < .0001). In freestanding children's hospitals, readmission after treatment of pediatric appendicitis is a relatively common and costly occurrence. Collaborative efforts are needed to characterize patient, treatment, and hospital-related risk factors as a basis for developing preventative strategies.", "The aim of this study was to determine the percentage of hospitals with adequate sample size to meaningfully compare performance by using the Agency for Healthcare Research and Quality (AHRQ) pediatric quality indicators (PDIs), which measure pediatric inpatient adverse events such as decubitus ulcer rate and infections due to medical care, have been nationally endorsed, and are currently publicly reported in at least 2 states. We performed a cross-sectional analysis of California hospital discharges from 2005-2007 for patients aged <18 years. For 9 hospital-level PDIs, after excluding discharges with PDIs indicated as present on admission, we determined for each PDI the volume of eligible pediatric patients for each measure at each hospital, the statewide mean rate, and the percentage of hospitals with adequate volume to identify an adverse event rate twice the statewide mean. Unadjusted California-wide event rates for PDIs during the study period (N = 2 333 556 discharges) were 0.2 to 38 per 1000 discharges. Event rates for specific measures were, for example, 0.2 per 1000 (iatrogenic pneumothorax in non-neonates), 19 per 1000 (postoperative sepsis), and 38 per 1000 (pediatric heart surgery mortality), requiring patient volumes of 49 869, 419, and 201 to detect an event rate twice the statewide average; 0%, 6.6%, and 25%, respectively, of California hospitals had this pediatric volume. Using these AHRQ-developed, nationally endorsed measures of the quality of inpatient pediatric care, one would not be able to identify many hospitals with performance 2 times worse than the statewide average due to extremely low event rates and inadequate pediatric hospital volume." ]
Technology in older adults: barriers and facilitators	This paper reports on the findings and recommendations specific to older adults from the "Tech Summit: Innovative Tools for Assessing Diet and Physical Activity for Health Promotion" forum organized by the North American branch of the International Life Sciences Institute. The summit aimed to investigate current and emerging challenges related to improving energy balance behavior assessment and intervention via technology. The current manuscript focuses on how novel technologies are applied in older adult populations and enumerated the barriers and facilitators to using technology within this population. Given the multiple applications for technology in this population, including the ability to monitor health events and behaviors in real time, technology presents an innovative method to aid with the changes associated with aging. Although older adults are often perceived as lacking interest in and ability to adopt technologies, recent studies show they are comfortable adopting technology and user uptake is high with proper training and guided facilitation. Finally, the conclusions suggest recommendations for future research, including the need for larger trials with clinical outcomes and more research using end-user design that includes older adults as technology partners who are part of the design process.	[ "Previous research has demonstrated a link between free-living accelerometer-measured breaks in sedentary time and health related variables. Breaks in sedentary time are typically inferred from time-stamped accelerometer data indicating a transition from lack of movement (recording of <100 activity counts/min) to relatively more movement (≥100 activity counts/min). However, it remains unknown whether these breaks actually represent sit-to-stand postural transitions in free-living. Thus, the purpose of this study was to compare free-living accelerometer-derived and posture-derived estimates of breaks in sedentary time using the ActiGraph GT3X+ (AG) and the activPAL™ (AP), respectively. A total of 15 participants concurrently wore an AG at their waist and an AP on their right thigh for 7 consecutive days (24h/day - removing them only when in contact with water). Data from both devices were matched on minute-by-minute timestamps while also applying a 3-min allowance window to account for clock drift. Dependent t-test was used to evaluate differences in mean breaks between AG and AP. The AG detected 74±4.1 breaks/day (mean±SEM) while the AP detected 39±3.1 breaks/day (P<0.001). On average, the AG detected 67% of the AP breaks while 65% of the AG breaks did not correspond with AP breaks. Of the non-corresponding AG breaks, 52% occurred when participants were sitting, 42% when standing, and 6% when transitioning from standing to sitting. The AG detected a significantly higher number of breaks in sedentary time, the majority of which do not correspond to sit-to-stand transitions as measured by the AP.", "Diabetes is the sixth leading cause of death and results in significant morbidity. The purpose of this study is to determine what demographic, health status, treatment, access/quality of care, and behavioral factors are associated with poor glycemic control in a Type 2 diabetic, low-income, minority, San Diego population. Longitudinal observational data was collected on patients with Type 2 diabetes from Project Dulce, a program in San Diego County designed to care for an underserved diabetic population. The study sample included 573 patients with a racial/ethnic mix of 53% Hispanic, 7% black, 18% Asian, 20% white, and 2% other. We utilized mixed effects models to determine the factors associated with poor glycemic control using hemoglobin A1C (A1C) as the outcome of interest. A multi-step model building process was used resulting in a final parsimonious model with main effects and interaction terms. Patients had a mean age of 55 years, 69% were female, the mean duration of diabetes was 7.1 years, 31% were treated with insulin, and 57% were obese. American Diabetes Association (ADA) recommendations for blood pressure and total cholesterol were met by 71% and 68%, respectively. Results of the mixed effects model showed that patients who were uninsured, had diabetes for a longer period of time, used insulin or multiple oral agents, or had high cholesterol had higher A1C values over time indicating poorer glycemic control. The younger subjects also had poorer control. This study provides factors that predict glycemic control in a specific low-income, multiethnic, Type 2 diabetic population. With this information, subgroups with high risk of disease morbidity were identified. Barriers that prevent these patients from meeting their goals must be explored to improve health outcomes.", "The aim of this paper is to present a participatory evaluation of an actual \"smart home\" project implemented in an independent retirement facility. Using the participatory evaluation process, residents guided the research team through development and implementation of the initial phase of a smart home project designed to assist residents to remain functionally independent and age in place. We recruited nine residents who provided permission to install the technology in their apartments. We conducted a total of 75 interviews and three observational sessions. Residents expressed overall positive perceptions of the sensor technologies and did not feel that these interfered with their daily activities. The process of adoption and acceptance of the sensors included three phases, familiarization, adjustment and curiosity, and full integration. Residents did not express privacy concerns. They provided detailed feedback and suggestions that were integrated into the redesign of the system. They also reported a sense of control resulting from their active involvement in the evaluation process. Observational sessions confirmed that the sensors were not noticeable and residents did not change their routines. The participatory evaluation approach not only empowers end-users but it also allows for the implementation of smart home systems that address residents' needs.", "We examined associations of sedentary time and sedentary accumulation patterns (ie, how sedentary time is accumulated) with prevalent diabetes in an ethnically diverse cohort of older women. Community-dwelling women aged 63-99 (n = 6,116; median age = 79) wore ActiGraph GT3X+ accelerometers 24 h/day for up to 7 days from which we derived average daily sedentary time and three measures of sedentary accumulation patterns: breaks in sedentary time, usual sedentary bout duration, and alpha. Odds ratios (ORs) and 95% confidence intervals (CIs) for prevalent diabetes were estimated using multivariable logistic regression. Twenty-one percent (n = 1,282) of participants had diabetes. Women in the highest quartile of sedentary time (≥10.3 h/day) had higher odds of diabetes (OR = 2.18; 95% CI = 1.77-2.70) than women in the lowest quartile (≤8.3 h/day). Prolonged accumulation patterns (ie, accumulating sedentary time in longer sedentary bouts) was associated with higher odds of diabetes than regularly interrupted patterns (comparing quartiles with the most vs least prolonged patterns: usual bout duration OR = 1.57, 95% CI = 1.28-1.92; alpha OR = 1.61, 95% CI = 1.32-1.97); however, there was no significant association for breaks in sedentary time (OR = 1.00, 95% CI = 0.82-1.20). High levels of sedentary time and accumulating it in prolonged patterns were associated with increased odds of diabetes among older women.", "We conducted a systematic review to investigate the cross-sectional and prospective associations of accelerometer-measured total sedentary time and breaks in sedentary time with individual cardiometabolic biomarkers in adults ≥18years of age. Ovid Medline, Embase, Web of Science and the Cochrane Library were searched for studies meeting the inclusion criteria. Due to inconsistencies in the measurement and analysis of sedentary time, data was synthesised and presented narratively rather than as a meta-analysis. Twenty-nine studies were included in the review; twenty-eight reported on total sedentary time and six on breaks in sedentary time. There was consistent evidence from cross-sectional data of an unfavourable association between total sedentary time and insulin sensitivity. There was also some evidence that total sedentary time was unfavourably associated with fasting insulin, insulin resistance and triglycerides. Furthermore, there was some evidence from cross-sectional data of a favourable association between breaks in sedentary time and triglycerides. Total sedentary time was consistently shown to be associated with poorer insulin sensitivity, even after adjusting for time spent in physical activity. This finding supports the proposed association between sedentary time and the development of Type 2 diabetes and reinforces the need to identify interventions to reduce time spent sedentary.", "This paper reports the association between self-reported diseases and impairments and 2-year onset of disability in a prospective study of people aged 65 years or older in five urban and rural centers in England and Wales (Medical Research Council Cognitive Function and Ageing Study; MRC-CFAS). We initially reviewed risk factors for onset of disability in 35 prospective studies of functional decline in older people published in 1998-2001. In the present study, disability was defined as requiring help from another person at least several times a week and was assessed by dependency in activities of daily living. Polytomous and bivariate logistic regression models were fitted for onset of disability and mortality among those nondisabled at baseline (n=7913), adjusting for age, sex, and sociodemography. Among prevalent conditions, arthritis (population-attributable risk 11.4%) and cognitive impairment indicated by a Mini-Mental State Examination score of <or=21 (population-attributable risk 6.8%) were powerful predictors of incident disability. Baseline cognitive impairment, stroke, treated diabetes, chronic airways obstruction, coronary heart disease, and treated hypertension were significantly associated with both incident disability and mortality, whereas Parkinson's disease, eyesight problems, and arthritis were statistically significant disabling conditions not associated with mortality. Stroke, heart attack, cognitive impairment, eyesight problems, and hearing problems were newly occurring conditions significantly associated with onset of disability. Cognitive impairment, arthritis, followed by stroke, and problems with vision have major impact on population disability at older ages. Both prevalent and incident conditions must be considered as risk factors to accurately assess potential benefits from prevention.", "The American Diabetes Association (ADA) \"Standards of Medical Care in Diabetes\" includes ADA's current clinical practice recommendations and is intended to provide the components of diabetes care, general treatment goals and guidelines, and tools to evaluate quality of care. Members of the ADA Professional Practice Committee, a multidisciplinary expert committee, are responsible for updating the Standards of Care annually, or more frequently as warranted. For a detailed description of ADA standards, statements, and reports, as well as the evidence-grading system for ADA's clinical practice recommendations, please refer to the Standards of Care Introduction Readers who wish to comment on the Standards of Care are invited to do so at professional.diabetes.org/SOC." ]
Sarcopenia and depressive symptoms in elderly Chinese community-dwelling individuals	The aim of this study was to assess the prevalence of sarcopenia and depressive symptoms and estimate the association between them in elderly Chinese community-dwelling individuals.	[ "to examine the clinical evidence reporting the prevalence of sarcopenia and the effect of nutrition and exercise interventions from studies using the consensus definition of sarcopenia proposed by the European Working Group on Sarcopenia in Older People (EWGSOP). PubMed and Dialog databases were searched (January 2000-October 2013) using pre-defined search terms. Prevalence studies and intervention studies investigating muscle mass plus strength or function outcome measures using the EWGSOP definition of sarcopenia, in well-defined populations of adults aged ≥50 years were selected. prevalence of sarcopenia was, with regional and age-related variations, 1-29% in community-dwelling populations, 14-33% in long-term care populations and 10% in the only acute hospital-care population examined. Moderate quality evidence suggests that exercise interventions improve muscle strength and physical performance. The results of nutrition interventions are equivocal due to the low number of studies and heterogeneous study design. Essential amino acid (EAA) supplements, including ∼2.5 g of leucine, and β-hydroxy β-methylbutyric acid (HMB) supplements, show some effects in improving muscle mass and function parameters. Protein supplements have not shown consistent benefits on muscle mass and function. prevalence of sarcopenia is substantial in most geriatric settings. Well-designed, standardised studies evaluating exercise or nutrition interventions are needed before treatment guidelines can be developed. Physicians should screen for sarcopenia in both community and geriatric settings, with diagnosis based on muscle mass and function. Supervised resistance exercise is recommended for individuals with sarcopenia. EAA (with leucine) and HMB may improve muscle outcomes.", "Fighting against inactivity and inadequate nutritional intake are of utmost importance in the elderly. To our knowledge, the few studies which have been performed were conducted for only a short period and the results do not permit formal conclusions to be drawn. We therefore tried to fill this gap in our knowledge by determining whether an intervention combining an acceptable progressive exercise programme and nutritional supplements would be feasible for a long-term period in the very frail elderly, and would bring about concomitant benefits in body composition and muscle power. Accordingly, this exercise and nutritional combination was assessed in the frail elderly in a 9-month randomised trial with a factorial design. Fifty-seven elderly volunteers over 72 years, from sixteen retirement homes in Lyon, France participated in the study. Dietary supplements were compared with placebo, and physical exercise was compared with memory training. Main outcome measures were fat-free mass (FFM) and muscle power. FFM was determined by labelled water, and muscle power was measured by a leg-extensor machine. At 9 months, the compliance was 63 % for exercise sessions, and 54 % for nutritional supplements. In patients with dietary supplements, muscle power increased by 57 % at 3 months (P=0.03), and showed only a tendency at 9 months; although FFM increased by 2.7 % at 9 months, the difference was not significant (P=0.10). Exercise did not improve muscle power at 9 months, but improved functional tests (five-time-chair rise, P=0.01). BMI increased with supplements (+3.65 %), but decreased with placebo (-0.5 %) at 9 months (P=0.007). A long-term combined intervention is feasible in frail elderly individuals with a good rate of compliance. Nutritional supplements and exercise may improve muscle function. Despite no significant results on FFM, due to the limited number of volunteers, combined intervention should be suggested to counteract muscle weakness in the frail elderly.", "A history of depression may increase risk for developing Alzheimer disease (AD) later in life. Clarifying this relation might improve understanding of risk factors for and disease mechanisms in AD. To systematically review and complete a meta-analysis on the relation of depression and AD. We conducted electronic bibliographic searches of MEDLINE, PsychLit, EMBASE, and BIOSIS using search terms sensitive to studies of etiology combined with searches on terms related to depression and AD and reviewed reference lists of articles. Studies with data contrasting depressed vs nondepressed patients who did and did not later develop AD were included. Studies that related continuous measures of depression and cognitive status were excluded. Numerical data were independently extracted by 3 reviewers. They also rated studies on a scale that assessed quality indicators for observational studies. Data on the interval between observation of depression and the diagnosis of AD were collected when available. Meta-analytic evaluation with random-effects models resulted in pooled odds ratios of 2.03 (95% confidence interval, 1.73-2.38) for case-control and of 1.90 (95% confidence interval, 1.55-2.33) for cohort studies. Findings of increased risk were robust to sensitivity analyses. Interval between diagnoses of depression and AD was positively related to increased risk of developing AD, suggesting that rather than a prodrome, depression may be a risk factor for AD. A history of depression may confer an increased risk for later developing AD. This relation may reflect an independent risk factor for the disease.", "Studies in young adults have demonstrated that beta-hydroxy-beta-methylbutyrate (HMB) can increase gains in strength and fat-free mass during a progressive resistance-training program. The purpose of this study was to determine whether HMB would similarly benefit 70-y-old adults undergoing a 5 d/wk exercise program. Thirty-one men (n = 15) and women (n = 16) (70 +/- 1 y) were randomly assigned in a double-blind study to receive either capsules containing a placebo or Ca-HMB (3 g/d) for the 8-wk study. Skin fold estimations of body composition as well as computerized tomography (CT) and dual X-ray absorptiometry (DXA) scans were measured before the study and immediately after the 8-wk training program. HMB supplementation tended to increase fat-free mass gain (HMB, 0.8 +/- 0.4 kg; placebo, -0.2 +/- 0.3 kg; treatment x time, P = 0.08). Furthermore, HMB supplementation increased the percentage of body fat loss (skin fold: HMB, -0.66 +/- 0.23%; placebo, -0.03 +/- 0.21%; P = 0.05) compared with the placebo group. CT scans also indicated a greater decrease in the percentage of body fat with HMB supplementation (P < 0.05). In conclusion, changes in body composition can be accomplished in 70-y-old adults participating in a strength training program, as previously demonstrated in young adults, when HMB is supplemented daily.", "There are few studies published that combine the interventions of physical training and nutrition. The aim of the present study was to describe the impact of a physical and nutritional intervention program for frail community- dwelling elderly people over the age of 75. Ninety-six community-dwelling elderly people (58 women) were randomized to four different groups: i) a physical training program (aerobic, muscle strength, balance), ii) a nutritional intervention program (individually targeted advice and group sessions), iii) a combination of these interventions, and iv) a control group. At baseline subjects were screened for physical performance such as muscle strength, balance, mobility and activities of daily living, as well as nutritional aspects such as energy intake, body weight and fat-free mass. These measurements were repeated immediately after the intervention, which lasted for 12 weeks, and after another 6 months. The intention-to-treat analysis indicated significant improvements in lower- extremity muscle strength in both training groups compared with the nutrition group at 1st follow-up. There were small significant changes for some of the balance measurements in the training group without nutrition treatment. The nutrition intervention did not show any significant results. This study shows the positive effect on lower-extremity muscle strength directly after the intervention. Balance training most probably needs to be more individualized in order to be effective for frail elderly people. Further studies are needed, with larger sample sizes, to investigate the effects of these types of interventions before any further conclusions can be drawn.", "Sarcopenia was recently classified a geriatric syndrome and is a major challenge to healthy aging. Affected patients tend to have worse clinical outcomes and higher mortality than those without sarcopenia. Although there is general agreement on the principal diagnostic characteristics, initial thresholds for muscle mass, strength, and physical performance were based on data from populations of predominantly Europid ancestry and may not apply worldwide. The Asian Working Group for Sarcopenia (AWGS) issued regional consensus guidelines in 2014, and many more research studies from Asia have since been published; this review summarizes recent progress. The prevalence of sarcopenia estimated by the AWGS criteria ranges between 4.1% and 11.5% of the general older population; however, prevalence rates were higher in Asian studies that used European Working Group on Sarcopenia in Older People cut-offs. Risk factors include age, sex, heart disease, hyperlipidemia, daily alcohol consumption, and low protein or vitamin intake; physical activity is protective. Adjusting skeletal muscle mass by weight rather than height is better in showing the effect of older age in sarcopenia and identifying sarcopenic obesity; however, some Asian studies found no significant skeletal muscle loss, and muscle strength might be a better indicator. Although AWGS 2014 diagnostic cut-offs were generally well accepted, some may require further revision in light of conflicting evidence from some studies. The importance of sarcopenia in diverse therapeutic areas is increasingly evident, with strong research interest in sarcopenic obesity and the setting of malignancy. Pharmacologic interventions have been unsatisfactory, and the core management strategies remain physical exercise and nutritional supplementation; however, further research is required to determine the most beneficial approaches.", "The purpose of this paper is to provide a comprehensive review of information accumulated over the past 26 years regarding the psychometric properties and utility of the Mini-Mental State Examination (MMSE). The reviewed studies assessed a wide variety of subjects, ranging from cognitively intact community residents to those with severe cognitive impairment associated with various types of dementing illnesses. The validity of the MMSE was compared against a variety of gold standards, including DSM-III-R and NINCDS-ADRDA criteria, clinical diagnoses, Activities of Daily Living measures, and other tests that putatively identify and measure cognitive impairment. Reliability and construct validity were judged to be satisfactory. Measures of criterion validity showed high levels of sensitivity for moderate-to-severe cognitive impairment and lower levels for mild degrees of impairment. Content analyses revealed the MMSE was highly verbal, and not all items were equally sensitive to cognitive impairment. Items measuring language were judged to be relatively easy and lacked utility for identifying mild language deficits. Overall, MMSE scores were affected by age, education, and cultural background, but not gender. In general, the MMSE fulfilled its original goal of providing a brief screening test that quantitatively assesses the severity of cognitive impairment and documents cognitive changes occurring over time. The MMSE should not, by itself, be used as a diagnostic tool to identify dementia. Suggestions for the clinical use of the MMSE are made." ]
Chymase is elevated and participates in tissue degeneration after permanent myocardial infarction	Chymase, a mast cell serine protease involved in the generation of multiple cardiovascular factors, such as angiotensin II and endothelin-1 (ET-1), is elevated and participates in tissue degeneration after permanent myocardial infarction (PMI). Anesthetized 4-month old male wild-type (WT) C57BL/6J mice and mouse mast cell protease-4 knockout (mMCP-4 KO) congeners were subjected to ligation of the left anterior descending (LAD) coronary artery. A group of mice was then subjected to Kaplan-Meier 28-day survival analysis. In another group of mice,	[ "Heart disease is a leading cause of death in adults. Here, we show that a few days after coronary artery ligation and reperfusion, the ischemia-injured heart elaborates the cardioprotective polypeptide, insulin-like growth factor-1 (IGF-1), which activates IGF-1 receptor prosurvival signaling and improves cardiac left ventricular systolic function. However, this signaling is antagonized by the chymase, mouse mast cell protease 4 (MMCP-4), which degrades IGF-1. We found that deletion of the gene encoding MMCP-4 (Mcpt4), markedly reduced late, but not early, infarct size by suppressing IGF-1 degradation and, consequently, diminished cardiac dysfunction and adverse structural remodeling. Our findings represent the first demonstration to our knowledge of tissue IGF-1 regulation through proteolytic degradation and suggest that chymase inhibition may be a viable therapeutic approach to enhance late cardioprotection in postischemic heart disease.", "Histamine, a product of mast cells, is an effective vasoconstrictor of atherosclerotic coronary arteries. Because it has been suggested that coronary spasm plays a role in acute coronary syndromes such as myocardial infarction (MI), we quantified and characterized the mast cells in the adventitia of infarct-related coronary arteries. In a series of 17 autopsied MI patients, we identified the segment of the left coronary artery with ruptured plaque responsible for the infarction. More distal segments from the infarct-related coronary artery, either with nonruptured plaques or with normal intima, were also studied. Corresponding segments taken from left coronary arteries obtained from 17 patients who had died of noncardiac causes served as controls. Adventitial mast cells in the infarct-related and the control coronary arteries were identified immunohistochemically by staining for tryptase. In the infarct-related coronary arteries, we also stained for chymase and histamine. Moreover, T lymphocytes and macrophages were identified immunohistochemically and counted. In the infarct-related coronary arteries, significantly larger numbers of mast cells were present in the adventitia backing ruptured plaques (98+/-40 mast cells/mm2, mean+/-SD) than in the adventitia backing nonruptured plaques (41+/-12 mast cells/mm2; P<0.001) or backing normal intima (19+/-8 mast cells/mm2; P<0.001). No such difference was found among the 3 different segments in the control coronary arteries. The majority of mast cells contained not only tryptase but also chymase. Mast cells were the only cells in the coronary adventitia that contained histamine. The proportion of adventitial mast cells that were degranulated was highest in the segments with ruptured plaques. The numbers of adventitial macrophages and T lymphocytes were also increased in the segments with plaque rupture. In infarct-related coronary arteries, the number of degranulated mast cells in the adventitia backing ruptured plaques is increased. Histamine released from the degranulated mast cells may reach the media, where it may locally provoke coronary spasm and thus contribute to the onset of MI.", "Insulin-like growth factor-1 (IGF-1) and its receptor (IGF-1R) are required for cell proliferation in vitro, raising the possibility that an autocrine IGF-1-IGF-1R system may be present in vivo and become activated in the viable ventricular myocytes shortly after infarction. Therefore, following the in vivo documentation of left ventricular failure in rats subjected to occlusion of the left coronary artery, the unaffected myocytes of the left ventricle were enzymatically dissociated and the expression of IGF-1R and IGF-1 mRNAs were measured at 12 h and at 1, 2-3, and 7 days after surgery. The level of expression of IGF-1R mRNA increased at 12 h and remained elevated at 1 and 2-3 days following coronary ligation. In addition, an increased level of IGF-1R protein on these cells was found. This phenomenon was coupled with the enhanced expression of IGF-1 mRNA in the muscle cells at all intervals. Myocardial infarction was also accompanied by an upregulation of proliferating cell nuclear antigen (PCNA) mRNA in myocytes and the detection of PCNA protein in nearly 1% of the cells. Similarly, bromodeoxyuridine labeling demonstrated that a comparable number of myocytes was positively stained. Finally, mitotic images in myocytes were observed. Thus, the IGF-1R-IGF-1 autocrine system may modulate myocyte cellular hyperplasia in the failing heart.", "Matrix metalloproteinase-9 (MMP-9) is prominently overexpressed after myocardial infarction (MI). We tested the hypothesis that mice with targeted deletion of MMP9 have less left ventricular (LV) dilation after experimental MI than do sibling wild-type (WT) mice. Animals that survived ligation of the left coronary artery underwent echocardiographic studies after MI; all analyses were performed without knowledge of mouse genotype. By day 8, MMP9 knockout (KO) mice had significantly smaller increases in end-diastolic and end-systolic ventricular dimensions at both midpapillary and apical levels, compared with infarcted WT mice; these differences persisted at 15 days after MI. MMP-9 KO mice had less collagen accumulation in the infarcted area than did WT mice, and they showed enhanced expression of MMP-2, MMP-13, and TIMP-1 and a reduced number of macrophages. We conclude that targeted deletion of the MMP9 gene attenuates LV dilation after experimental MI in mice. The decrease in collagen accumulation and the enhanced expression of other MMPs suggest that MMP-9 plays a prominent role in extracellular matrix remodeling after MI.", "The objective of the study was to determine whether the extent of left ventricular scar, measured with delayed hyperenhancement cardiac magnetic resonance (DHE-CMR), predicts survival in patients with ischemic cardiomyopathy (ICM) and severely reduced left ventricular ejection fraction (LVEF). Patients with ICM and reduced LVEF have poor survival. Such patients have a high myocardial scar burden. CMR is highly accurate in delineation of myocardial scar. We studied 349 patients (76% men) with severe ICM (>or=70% disease in >or=1 epicardial coronary, and mean LVEF of 24%) that underwent DHE-CMR (Siemens 1.5-T scanner, Erlangen, Germany), between 2003 and 2006. Scar (quantified as percentage of myocardium) was defined on DHE-MR images as an intensity >2 standard deviations above the viable myocardium. Transmurality score was semiquantitatively recorded in a 17-segment model as: 0 = no scar, 1 = 1% to 25% scar, 2 = 26% to 50%, 3 = 51% to 75%, and 4 = >75%. The LVEF, demographic data, risk factors, need for cardiac transplantation (CTx), and all-cause mortality were recorded. The mean age and follow-up were 65 +/- 11 years and 2.6 +/- 1.2 years (median 2.4 years [1.1, 3.5]), respectively. There were 56 events (51 deaths and 5 CTx). Mean scar percentage and transmurality score were higher in patients with events versus those without (39 +/- 22 vs. 30 +/- 20, p = 0.003, and 9.7 +/- 5 vs. 7.8 +/- 5, p = 0.004). On Cox proportional hazard survival analysis, quantified scar was greater than the median (30% of total myocardium), and female gender predicted events (relative risk 1.75 [95% Confidence Interval: 1.02 to 3.03] and relative risk 1.83 [95% Confidence Interval: 1.06 to 3.16], respectively, both p = 0.03). In patients with ICM and severely reduced LVEF, a greater extent of myocardial scar, delineated by DHE-CMR is associated with increased mortality or the need for cardiac transplantation, potentially aiding further risk-stratification.", "The current study examined the contributions of angiotensin-converting enzyme (ACE) vs. chymase to angiotensin II (ANG II) generation in membrane preparations from left ventricles of humans, dogs, rabbits, and rats and from total heart of mice. ACE and chymase activity were measured in membrane preparations extracted with low or high detergent (LD and HD, respectively) concentrations. We hypothesized that ACE, which is membrane bound in vivo, would be preferentially localized to the HD preparation, whereas chymase, which is localized to the cytoplasm and cardiac interstitium, would be localized to the LD preparation. In human heart, ACE activity was 16-fold higher in the HD than in the LD preparation, whereas chymase activity was 15-fold higher in the LD than in the HD preparation. Total ANG II formation was greater in human heart [15.8 +/- 3.4 (SE) micromol ANG II x g(-1) x min(-1)] than in dog, rat, rabbit, and mouse hearts (3.90 +/- 0.35, 0.41 +/- 0.02, 0.61 +/- 0.07, and 1.16 +/- 0.08 micromol ANG II x g(-1) x min(-1), respectively, P < 0.05, by analysis of variance). ANG II formation from ACE was higher in mouse heart (1.09 +/- 0.05 micromol ANG II x g(-1) x min(-1), p < 0.001) than in rabbit, human, dog, and rat hearts (0.55 +/- 0.06, 0.34 +/- 0.01, 0.32 +/- 0.06, and 0.31 +/- 0.02 micromol ANG II x g(-1) x min(-1), respectively). In contrast, chymase activity was higher in human heart (15.3 +/- 3.4 micromol ANG II x g(-1) x min(-1)) than in dog, rat, rabbit, and mouse hearts (3.59 +/- 0.29, 0.10 +/- 0.01, 0.06 +/- 0.01, and 0.07 +/- 0.01 micromol ANG II x g(-1) x min(-1), respectively). Our results demonstrate important species differences in the pathways of intracardiac ANG II generation. Chymase predominated over ACE activity in human heart, accounting for extremely high total ANG II formation in human heart compared with dog, rat, rabbit, and mouse hearts.", "Recent studies have demonstrated that hamsters, like humans, possess both angiotensin converting enzyme (ACE)- and chymase-dependent angiotensin (Ang) II-forming pathways in cardiovascular tissues. We recently found that, after myocardial infarction (MI) in hamsters, cardiac chymase was significantly activated. In order to determine whether suppression of cardiac chymase activity could provide prognostic benefit after MI, we examined the effects of NK3201, a novel, orally active and specific chymase inhibitor, on cardiac function and survival during the acute phase of MI in hamsters. Two hundred and ten male Syrian hamsters were used in the present study. The left coronary artery of each hamster was ligated to induce MI. NK3201 at a dose of 30 mg/kg per day was administered orally by gastric gavage, starting either 3 days before or 1 day after MI. ACE and chymase activities were significantly increased in the infarcted left ventricle 3 days after MI. NK3201 treatment starting 3 days before MI significantly inhibited the increase in cardiac chymase activity, while it did not affect ACE activity either in plasma or in heart 3 days after MI. A significant improvement in cardiac function was observed 3 and 14 days after MI in the group receiving NK3201. Compared with vehicle treatment, NK3201 treatment initiated either 3 days before or 1 day after MI significantly reduced the mortality rate during the 14 days of observation following MI. These findings indicate that cardiac chymase plays an important role after MI and this finding may provide a novel therapeutic target in post-MI treatment.", "The mast cell is one of the major effector cells in inflammatory reactions and can be found in most tissues throughout the body. During inflammation, an increase in the number of mast cells can be seen, e.g., in the intraepithelial cell layer after a provoked allergic reaction. Such accumulation probably requires directed migration of mature mast cells or their precursors. To study the migration of human mast cells we used as a model the human mast cell line, HMC-1, and stem cell factor-dependent (also referred to as mast cell growth factor or Kit ligand) cord blood-derived mast cells. The results show that stem cell factor is a potent chemotactic factor for human mast cells in vitro. The chemotactic response to SCF was found to be dose dependent, reaching a maximum at 50 ng/ml. The activity of SCF could be blocked by anti-SCF Abs. We also tested the effect of different intercrines, i.e., IL-8, MIP-1 alpha, MIP-1 beta, RANTES, and MCAF (also referred to as monocyte chemotactic protein 1), on human mast cell migration. Only RANTES was chemotactic for in vitro-developed mast cells. None of the tested intercrines induced migration of HMC-1 cells. For migration, the mast cells were dependent on binding to an extracellular matrix protein. Thus, coating of the filters with fibronectin was required, whereas collagen or laminin did not promote migration. Adhesion of HMC-1 cells to fibronectin could also be shown in an adhesion assay. In addition, expression of receptors for fibronectin could be detected on the surface of the mast cells. These results show that SCF is not only a growth and differentiation factor for human mast cells in vitro but also a potent chemoattractant for such cells.", "Nitrite has emerged as an endogenous signaling molecule with potential therapeutic implications for cardiovascular disease. Steady-state levels of nitrite are derived in part from dietary sources; therefore, we investigated the effects of dietary nitrite and nitrate supplementation and deficiency on NO homeostasis and on the severity of myocardial ischemia-reperfusion (MI/R) injury. Mice fed a standard diet with supplementation of nitrite (50 mg/liter) in their drinking water for 7 days exhibited significantly higher plasma levels of nitrite, exhibited significantly higher myocardial levels of nitrite, nitroso, and nitrosyl-heme, and displayed a 48% reduction in infarct size (Inf) after MI/R. Supplemental nitrate (1 g/liter) in the drinking water for 7 days also increased blood and tissue NO products and significantly reduced Inf. A time course of ischemia-reperfusion revealed that nitrite was consumed during the ischemic phase, with an increase in nitroso/nitrosyl products in the heart. Mice fed a diet deficient in nitrite and nitrate for 7 days exhibited significantly diminished plasma and heart levels of nitrite and NO metabolites and a 59% increase in Inf after MI/R. Supplementation of nitrite in the drinking water for 7 days reversed the effects of nitrite deficiency. These data demonstrate the significant influence of dietary nitrite and nitrate intake on the maintenance of steady-state tissue nitrite/nitroso levels and illustrate the consequences of nitrite deficiency on the pathophysiology of MI/R injury. Therefore, nitrite and nitrate may serve as essential nutrients for optimal cardiovascular health and may provide a treatment modality for cardiovascular disease." ]
Necrotising glomerulonephritis associated with cocaine abuse: a case report	Cocaine adulterated levamisole is an increasingly reported cause of skin necrosis, arthralgia and systemic vasculitis, but renal involvement is uncommon. We present a case of a 40-year-old Hispanic man with a history of cocaine abuse who presented with acute kidney injury to the rheumatology clinic where he was being treated for chronic inflammatory arthritis. He was found to have a serum creatinine of 2.5 mg/dL, microscopic haematuria and subnephrotic proteinuria, along with positive proteinase 3, myeloperoxidase, anticardiolipin antibodies and an elevated antinuclear antibody titre. The renal pathology revealed focal necrotising glomerulonephritis with crescentic features and mild immune type deposition. The patient was treated with cocaine abstinence, pulse dose steroids followed by maintenance prednisone, rituximab and cyclophosphamide. His renal function subsequently improved but did not normalise. We believe that his incomplete improvement was due to the degree of kidney injury on presentation as well as recidivism with cocaine use.	[ "A group of pauci-immune vasculitides, characterized by neutrophil-rich necrotizing inflammation of small vessels and the presence of antineutrophil cytoplasmic antibodies (ANCAs), is referred to as ANCA-associated vasculitis (AAV). ANCAs against proteinase 3 (PR3) (PR3-ANCA) or myeloperoxidase (MPO) (MPO-ANCA) are found in over 90% of patients with active disease, and these ANCAs are implicated in the pathogenesis of AAV. Dying neutrophils surrounding the walls of small vessels are a histological hallmark of AAV. Traditionally, it has been assumed that these neutrophils die by necrosis, but neutrophil extracellular traps (NETs) have recently been visualized at the sites of vasculitic lesions. AAV patients also possess elevated levels of NETs in the circulation. ANCAs are capable of inducing NETosis in neutrophils, and their potential to do so has been shown to be affinity dependent and to correlate with disease activity. Neutrophils from AAV patients are also more prone to release NETs spontaneously than neutrophils from healthy blood donors. NETs contain proinflammatory proteins and are thought to contribute to vessel inflammation directly by damaging endothelial cells and by activating the complement system and indirectly by acting as a link between the innate and adaptive immune system through the generation of PR3- and MPO-ANCA. Injection of NET-loaded myeloid dendritic cells into mice results in circulating PR3- and MPO-ANCA and the development of AAV-like disease. NETs have also been shown to be essential in a rodent model of drug-induced vasculitis. NETs induced by propylthiouracil could not be degraded by DNaseI, implying that disordered NETs might be important for the generation of ANCAs. NET degradation was also highlighted in another study showing that AAV patients have reduced DNaseI activity resulting in less NET degradation. With this in mind, it might be that prolonged exposure to proteins in the NETs due to the overproduction of NETs and/or reduced clearance of NETs is important in AAV. However, not all ANCAs are pathogenic and some might possibly also aid in the clearance of NETs. A dual role for ANCAs in relation to circulating NET levels has been proposed because a negative correlation was observed between PR3-ANCA and NET remnants in patients in remission.", "To describe the clinical and serologic abnormalities in 6 patients who presented with retiform purpura and extensive cutaneous necrosis after exposure to levamisole-adulterated cocaine. All patients were evaluated at San Francisco General Hospital or the University of California San Francisco Medical Center. Each underwent standard screening for substances of abuse and had urine tested for the presence of levamisole by liquid chromatography tandem mass spectrometry. Routine laboratory, autoantibody, and antiphospholipid antibody testing was performed in the hospitals' clinical or reference laboratories. Testing for atypical antineutrophil cytoplasmic antibodies (ANCAs) was performed separately using commercially available enzyme-linked immunosorbent assay kits. The patients were women ages 39-50 years who presented with retiform purpura and cutaneous necrosis. Skin biopsies revealed a predominantly small-vessel thrombotic vasculopathy with varying degrees of vasculitis. Four patients were neutropenic. All tested positive for lupus anticoagulant, had IgM antibodies to cardiolipin, and tested strongly positive for ANCAs in a perinuclear pattern by immunofluorescence. Each patient had antibodies to multiple components of neutrophil granules, including neutrophil elastase, lactoferrin, cathepsin G, proteinase 3, and myeloperoxidase. Rheumatologists should be aware of this distinctive form of necrotic purpura, its associated autoantibodies, and its link to levamisole-adulterated cocaine.", "Levamisole is an immunomodulatory agent that was used to treat various cancers before being withdrawn from the United States market in 2000 because of adverse effects. Levamisole is currently approved as an antihelminthic agent in veterinary medicine, but is also being used illicitly as a cocaine adulterant. Potential complications associated with use of levamisole-laced cocaine include neutropenia, agranulocytosis, arthralgias, retiform purpura, and skin necrosis. Treatment is primarily supportive, and skin lesions typically resolve with cessation of cocaine use. The incidence of hospitalizations related to use of levamisole-contaminated cocaine continues to increase and clinicians should be aware of the more common clinical manifestations.", "A new gas chromatographic method was developed for the quantification of levamisole in human plasma and urine, using a nitrogen-phosphorus flame ionization detector. The adsorption of the drug onto glass was prevented by treating the glassware with a siliconizing agent. The sensitivity of the assay was 10 ng ml-1 and as low as 2 ng ml-1 can be detected in plasma. The urinary metabolite p-hydroxylevamisole was analysed by high performance liquid chromatography with ultraviolet detection. The sensitivity of this assay was 0.50 micrograms ml-1. Plasma and urinary concentrations of levamisole were determined in 10 healthy volunteers including seven men and three women following the administration of a single 150 mg dose of levamisole. Levamisole was rapidly absorbed (tmax 1.5 h), giving a peak plasma concentration of 716.7 +/- 217.5 ng ml-1. The plasma elimination half-life of levamisole was 5.6 +/- 2.5 h. Only 3.2 +/- 2.9 per cent of the oral dose was recovered as unchanged drug in the urine, suggesting the importance of clearance of levamisole by routes other than the kidney, and most probably by hepatic metabolism. The urinary concentrations of p-hydroxylevamisole were determined before and after hydrolysis of the urine samples with beta-glucuronidase, and the level of conjugation of the metabolite with glucuronic acid was then estimated. Cumulative recovery of the metabolite accounted for 1.6 +/- 1.1 per cent and 12.4 +/- 5.5 per cent of the oral dose of levamisole before and after hydrolysis, respectively, indicating that p-hydroxylation is a relatively important route of metabolism of levamisole, and that the p-hydroxylated metabolite is excreted mainly in conjugation with glucuronic acid. Except for the absorption rate of levamisole which is approximately twice as rapid in women as in men, there is no marked difference in the pharmacokinetics of levamisole between healthy men and women.", "We present a child on long-term treatment with levamisole, and heterozygous for factor V Leiden, who developed cutaneous necrosis associated with formation of p-ANCA and lupus anticoagulant. Symptoms resolved when the levamisole treatment was stopped." ]
aluminum-activated malate transporters	Aluminum-activated malate transporters (	[ "Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes (http://www. ncbi.nlm. nih.gov/COG). The COGs were constructed by applying the criterion of consistency of genome-specific best hits to the results of an exhaustive comparison of all protein sequences from these genomes. The database comprises 2091 COGs that include 56-83% of the gene products from each of the complete bacterial and archaeal genomes and approximately 35% of those from the yeast Saccharomyces cerevisiae genome. The COG database is accompanied by the COGNITOR program that is used to fit new proteins into the COGs and can be applied to functional and phylogenetic annotation of newly sequenced genomes.", "Over 35 years ago, Susumu Ohno stated that gene duplication was the single most important factor in evolution. He reiterated this point a few years later in proposing that without duplicated genes the creation of metazoans, vertebrates, and mammals from unicellular organisms would have been impossible. Such big leaps in evolution, he argued, required the creation of new gene loci with previously nonexistent functions. Bold statements such as these, combined with his proposal that at least one whole-genome duplication event facilitated the evolution of vertebrates, have made Ohno an icon in the literature on genome evolution. However, discussion on the occurrence and consequences of gene and genome duplication events has a much longer, and often neglected, history. Here we review literature dealing with the occurrence and consequences of gene duplication, beginning in 1911. We document conceptual and technological advances in gene duplication research from this early research in comparative cytology up to recent research on whole genomes, \"transcriptomes,\" and \"interactomes.\"", "A total of 355 simple sequence repeat (SSR) markers were developed, based on expressed sequence tag (EST) and bacterial artificial chromosome (BAC)-end sequence databases, and successfully used to construct an SSR-based genetic linkage map of the apple. The consensus linkage map spanned 1143 cM, with an average density of 2.5 cM per marker. Newly developed SSR markers along with 279 SSR markers previously published by the HiDRAS project were further used to integrate physical and genetic maps of the apple using a PCR-based BAC library screening approach. A total of 470 contigs were unambiguously anchored onto all 17 linkage groups of the apple genome, and 158 contigs contained two or more molecular markers. The genetically mapped contigs spanned ∼421 Mb in cumulative physical length, representing 60.0% of the genome. The sizes of anchored contigs ranged from 97 kb to 4.0 Mb, with an average of 995 kb. The average physical length of anchored contigs on each linkage group was ∼24.8 Mb, ranging from 17.0 Mb to 37.73 Mb. Using BAC DNA as templates, PCR screening of the BAC library amplified fragments of highly homologous sequences from homoeologous chromosomes. Upon integrating physical and genetic maps of the apple, the presence of not only homoeologous chromosome pairs, but also of multiple locus markers mapped to adjacent sites on the same chromosome was detected. These findings demonstrated the presence of both genome-wide and segmental duplications in the apple genome and provided further insights into the complex polyploid ancestral origin of the apple.", "MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/.", "The transient gene expression system using Arabidopsis mesophyll protoplasts has proven an important and versatile tool for conducting cell-based experiments using molecular, cellular, biochemical, genetic, genomic and proteomic approaches to analyze the functions of diverse signaling pathways and cellular machineries. A well-established protocol that has been extensively tested and applied in numerous experiments is presented here. The method includes protoplast isolation, PEG-calcium transfection of plasmid DNA and protoplast culture. Physiological responses and high-throughput capability enable facile and cost-effective explorations as well as hypothesis-driven tests. The protoplast isolation and DNA transfection procedures take 6-8 h, and the results can be obtained in 2-24 h. The cell system offers reliable guidelines for further comprehensive analysis of complex regulatory mechanisms in whole-plant physiology, immunity, growth and development.", "We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.", "A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome." ]
CHOMP: a composable protein-protein regulation system	Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.	[ "A recurring theme in biological circuits is the existence of components that are antagonistically bifunctional, in the sense that they simultaneously have two opposing effects on the same target or biological process. Examples include bifunctional enzymes that carry out two opposing reactions such as phosphorylating and dephosphorylating the same target, regulators that activate and also repress a gene in circuits called incoherent feedforward loops, and cytokines that signal immune cells to both proliferate and die. Such components are termed \"paradoxical\", and in this review we discuss how they can provide useful features to cell circuits that are otherwise difficult to achieve. In particular, we summarize how paradoxical components can provide robustness, generate temporal pulses, and provide fold-change detection, in which circuits respond to relative rather than absolute changes in signals.", "Hepatitis C virus (HCV) possesses a positive-sense RNA genome which encodes a large polyprotein of 3,010 amino acids. Previous data and sequence analysis have indicated that this polyprotein is processed by cellular proteases and possibly by a virally encoded serine protease localized in the N-terminal domain of nonstructural protein NS3. To characterize the molecular aspects of HCV protein biogenesis and to clearly identify the protein products derived from the HCV genome, we have examined HCV polyprotein expression by using the vaccinia virus T7 transient expression system in transfected cells and by cell-free translation studies. HCV proteins were identified by immunoprecipitation with region-specific antisera. Here we show that the amino-terminal region of the HCV polyprotein is processed in vitro by cellular proteases releasing three structural proteins: p21 (core), gp37 (E1), and gp61 (E2). Processing of the nonstructural region of HCV was evident in transfected cells. Two proteins of 24 and 68 kDa were immunoprecipitated with anti-NS2 and NS3 antisera, respectively. Antiserum against NS4 recognized three proteins of 6, 26, and 31 kDa, while antisera specific for NS5 immunoprecipitated two polypeptides of 56 and 65 kDa, indicating that each of these two genes encodes at least two different proteins. When the NS3 protease domain was inactivated by replacing the proposed catalytic Ser-1165 with Ala, processing at several sites was abolished. When Ser-1164 was mutated to Ala, no effect on the processing was observed. Cleavage activities at three of the four sites affected by NS3 were shown to occur in trans, while processing at the carboxy terminus of NS3 could not be mediated in trans. These results provide a detailed description of the protein products obtained from the processing of the HCV polyprotein. Furthermore, the data obtained implicate NS3 as a serine protease and demonstrate that a catalytically active NS3 is necessary for cleavage of the nonstructural region of HCV.", "The bottom-up design of protein-based signaling networks is a key goal of synthetic biology; yet, it remains elusive due to our inability to tailor-make signal transducers and receptors that can be readily compiled into defined signaling networks. Here, we report a generic approach for the construction of protein-based molecular switches based on artficially autoinhibited proteases. Using structure-guided design and directed protein evolution, we created signal transducers based on artificially autoinhibited proteases that can be activated following site-specific proteolysis and also demonstrate the modular design of an allosterically regulated protease receptor following recombination with an affinity clamp peptide receptor. Notably, the receptor's mode of action can be varied from >5-fold switch-OFF to >30-fold switch-ON solely by changing the length of the connecting linkers, demonstrating a high functional plasticity not previously observed in naturally occurring receptor systems. We also create an integrated signaling circuit based on two orthogonal autoinhibited protease units that can propagate and amplify molecular queues generated by the protease receptor. Finally, we present a generic two-component receptor architecture based on proximity-based activation of two autoinhibited proteases. Overall, the approach allows the design of protease-based signaling networks that, in principle, can be connected to any biological process.", "The serine proteinase of hepatitis C virus (HCV) non-structural protein NS3 was efficiently expressed in an active form as a fused protein with oligohistidine in Escherichia coli. The recombinant fusion protein was purified to near homogeneity by affinity chromatography on a metal chelation column. Trans-cleavage activity of this protein was investigated by using the substrate NS5 protein expressed in insect cells. The purified serine proteinase trans-cleaved the partially purified NS5 protein. In contrast, the NS3 proteins with mutations at the proposed catalytic site, Ser1165 or His1083, lost the trans-cleavage activity. Analysis of the authentic enzyme and variants with site-directed mutations provides a useful tool for understanding the structure-function relationship of the NS3 serine proteinase. We then developed an in vivo trans-cleavage assay system by coexpression of the NS3 proteinase and the NS5 substrate in E coli, and examined the effect of known inhibitors of serine proteinase. Inhibition of its proteolytic activity by N-p-tosyl-L-lysine chloromethyl ketone (TLCK) was observed, but only at high concentrations. The in vitro and in vivo trans-cleavage assays for NS3 serine proteinase will facilitate efficient testing for inhibitors of the replication of HCV and specific treatment for hepatitis C.", "Hepatitis C virus (HCV) is a major causative agent of posttransfusion non-A, non-B hepatitis, which often develops into malignant chronic diseases, including liver cirrhosis and hepatocellular carcinoma. We have cloned from human carriers overlapping cDNAs (9,416 bp) covering the entire coding region of the HCV genome. The latter encodes a 3,010-amino-acid polyprotein. In addition, there are 332 and 54 bases of 5' and 3' noncoding sequences, respectively. Our HCV strain has a 77% nucleic acid identity to the HCV strain cloned by workers at Chiron Corporation. The hydrophobicity profile of the putative polyprotein is similar to those of flaviviruses, but it has limited amino acid homology to polyproteins of flaviviruses and other viruses, indicating that HCV is at most distantly related to flaviviruses.", "G-protein-coupled receptors (GPCRs) are the largest and most diverse group of membrane receptors in eukaryotes and detect a wide array of cues in the human body. Here we describe a molecular device that couples CRISPR-dCas9 genome regulation to diverse natural and synthetic extracellular signals via GPCRs. We generate alternative architectures for fusing CRISPR to GPCRs utilizing the previously reported design, Tango, and our design, ChaCha. Mathematical modeling suggests that for the CRISPR ChaCha design, multiple dCas9 molecules can be released across the lifetime of a GPCR. The CRISPR ChaCha is dose-dependent, reversible, and can activate multiple endogenous genes simultaneously in response to extracellular ligands. We adopt the design to diverse GPCRs that sense a broad spectrum of ligands, including synthetic compounds, chemokines, mitogens, fatty acids, and hormones. This toolkit of CRISPR-coupled GPCRs provides a modular platform for rewiring diverse ligand sensing to targeted genome regulation for engineering cellular functions.", "The NS3 proteinase of hepatitis C virus utilizes NS4A as a cofactor for cleavages at four sites (3/4A, 4A/4B, 4B/5A, and 5A/5B) in the nonstructural region of the viral polyprotein. To characterize NS4A for its role in modulating the NS3 proteinase activity at various cleavage sites, synthetic peptides spanning various parts of NS4A were synthesized and tested in a cell-free trans-cleavage reaction using purified NS3 proteinase domain and polyprotein substrates. The NS3 proteinase domain was expressed in Escherichia coli, purified, denatured, and refolded to an enzymatically active form. We found that a 12-amino-acid peptide containing amino acid residues 22 to 33 in NS4A (CVVIVGRIVLSG) was sufficient for cofactor activity in NS3-mediated proteolysis. The peptide enhanced the cleavage at the NS5A/5B site and was necessary for NS3-mediated cleavage at NS4A/4B and NS4B/5A. Sequential amino acid substitution within the designated peptide identified residues I29 and I25 as critical for potential cofactor activity. We provide evidence that the NS4A peptide and the NS3 catalytic domain form an enzymatically active complex. These data suggest that the central 12-amino-acid peptide (aa 22-33) of NS4A is primarily important for the cofactor activity through complex formation with NS3, and the interaction may represent a new target for antiviral drug development." ]
A Data-Driven Framework to Assess the Level of Consciousness in Comatose Patients	We devise a data-driven framework to assess the level of consciousness in etiologically heterogeneous comatose patients using intrinsic dynamical changes of resting-state Electroencephalogram (EEG) signals.	[ "Neuronal aggregates involved in conscious awareness are not evenly distributed throughout the CNS but comprise key components referred to as the neural network correlates of consciousness (NNCC). A critical node in this network is the posterior cingulate, precuneal, and retrosplenial cortices. The cytological and neurochemical composition of this region is reviewed in relation to the Brodmann map. This region has the highest level of cortical glucose metabolism and cytochrome c oxidase activity. Monkey studies suggest that the anterior thalamic projection likely drives retrosplenial and posterior cingulate cortex metabolism and that the midbrain projection to the anteroventral thalamic nucleus is a key coupling site between the brainstem system for arousal and cortical systems for cognitive processing and awareness. The pivotal role of the posterior cingulate, precuneal, and retrosplenial cortices in consciousness is demonstrated with posterior cingulate epilepsy cases, midcingulate lesions that de-afferent this region and are associated with unilateral sensory neglect, observations from stroke and vegetative state patients, alterations in blood flow during sleep, and the actions of general anesthetics. Since this region is critically involved in self reflection, it is not surprising that it is similarly a site for the NNCC. Interestingly, information processing during complex cognitive tasks and during aversive sensations such as pain induces efforts to terminate self reflection and result in decreased processing in posterior cingulate and precuneal cortices.", "The goal of the present study was to investigate the correlation of mismatch negativity (MMN) to other biological and clinical measures in schizophrenic patients using Quantitative electroencepharography (QEEG), computed tomography (CT), and psychopathological ratings. MMN was recorded during an auditory oddball paradigm. QEEG was recorded in the resting condition. Additionally, areas of the lateral ventricles and Sylvian fissure were measured using CT. Although the authors could not obtain a significant difference in MMN amplitudes between controls and the schizophrenic patients, MMN deflection inversely correlated with slow wave QEEG power and dilation of the lateral ventricles. Furthermore, the longer the duration of illness, the lower the MMN amplitudes and the larger the SF-BR in the patients. However there was no significant correlation between illness duration and QEEG. In this view, a correlation between MMN and the delta power in QEEG might usefully suggest a progression in pathology of first manifestation of psychosis. The patients with reduced MMN accompanied by greater slow waves even at their first manifestation might have severely progressing pathological process and poor prognosis of disease outcome.", "Disorders of Consciousness (DOC) like Vegetative State (VS), and Minimally Conscious State (MCS) are clinical conditions characterized by the absence or intermittent behavioral responsiveness. A neurophysiological monitoring of parameters like Event-Related Potentials (ERPs) could be a first step to follow-up the clinical evolution of these patients during their rehabilitation phase. Eleven patients diagnosed as VS (n = 8) and MCS (n = 3) by means of the JFK Coma Recovery Scale Revised (CRS-R) underwent scalp EEG recordings during the delivery of a 3-stimuli auditory oddball paradigm, which included standard, deviant tones and the subject own name (SON) presented as a novel stimulus, administered under passive and active conditions. Four patients who showed a change in their clinical status as detected by means of the CRS-R (i.e., moved from VS to MCS), were subjected to a second EEG recording session. All patients, but one (anoxic etiology), showed ERP components such as mismatch negativity (MMN) and novelty P300 (nP3) under passive condition. When patients were asked to count the novel stimuli (active condition), the nP3 component displayed a significant increase in amplitude (p = 0.009) and a wider topographical distribution with respect to the passive listening, only in MCS. In 2 out of the 4 patients who underwent a second recording session consistently with their transition from VS to MCS, the nP3 component elicited by passive listening of SON stimuli revealed a significant amplitude increment (p < 0.05). Most relevant, the amplitude of the nP3 component in the active condition, acquired in each patient and in all recording sessions, displayed a significant positive correlation with the total scores (p = 0.004) and with the auditory sub-scores (p < 0.00001) of the CRS-R administered before each EEG recording. As such, the present findings corroborate the value of ERPs monitoring in DOC patients to investigate residual unconscious and conscious cognitive function.", "Functional neuroimaging studies have started unravelling unexpected functional attributes for the posteromedial portion of the parietal lobe, the precuneus. This cortical area has traditionally received little attention, mainly because of its hidden location and the virtual absence of focal lesion studies. However, recent functional imaging findings in healthy subjects suggest a central role for the precuneus in a wide spectrum of highly integrated tasks, including visuo-spatial imagery, episodic memory retrieval and self-processing operations, namely first-person perspective taking and an experience of agency. Furthermore, precuneus and surrounding posteromedial areas are amongst the brain structures displaying the highest resting metabolic rates (hot spots) and are characterized by transient decreases in the tonic activity during engagement in non-self-referential goal-directed actions (default mode of brain function). Therefore, it has recently been proposed that precuneus is involved in the interwoven network of the neural correlates of self-consciousness, engaged in self-related mental representations during rest. This hypothesis is consistent with the selective hypometabolism in the posteromedial cortex reported in a wide range of altered conscious states, such as sleep, drug-induced anaesthesia and vegetative states. This review summarizes the current knowledge about the macroscopic and microscopic anatomy of precuneus, together with its wide-spread connectivity with both cortical and subcortical structures, as shown by connectional and neurophysiological findings in non-human primates, and links these notions with the multifaceted spectrum of its behavioural correlates. By means of a critical analysis of precuneus activation patterns in response to different mental tasks, this paper provides a useful conceptual framework for matching the functional imaging findings with the specific role(s) played by this structure in the higher-order cognitive functions in which it has been implicated. Specifically, activation patterns appear to converge with anatomical and connectivity data in providing preliminary evidence for a functional subdivision within the precuneus into an anterior region, involved in self-centred mental imagery strategies, and a posterior region, subserving successful episodic memory retrieval.", "The concept of consciousness continues to defy definition and elude the grasp of philosophical and scientific efforts to formulate a testable construct that maps to human experience. Severe acquired brain injury results in the dissolution of consciousness, providing a natural model from which key insights about consciousness may be drawn. In the clinical setting, neurologists and neurorehabilitation specialists are called on to discern the level of consciousness in patients who are unable to communicate through word or gesture, and to project outcomes and recommend approaches to treatment. Standards of care are not available to guide clinical decision-making for this population, often leading to inconsistent, inaccurate and inappropriate care. In this Review, we describe the state of the science with regard to clinical management of patients with prolonged disorders of consciousness. We review consciousness-altering pathophysiological mechanisms, specific clinical syndromes, and novel diagnostic and prognostic applications of advanced neuroimaging and electrophysiological procedures. We conclude with a provocative discussion of bioethical and medicolegal issues that are unique to this population and have a profound impact on care, as well as raising questions of broad societal interest.", "Recently, blink-related delta oscillations (delta BROs) have been observed in healthy subjects during spontaneous blinking at rest. Delta BROs have been linked with continuous gathering of information from the surrounding environment, which is classically attributed to the precuneus. Furthermore, fMRI studies have shown that precuneal activity is reduced or missing when consciousness is low or absent. We therefore hypothesized that the source of delta BROs in healthy subjects could be located in the precuneus and that delta BROs could be absent or reduced in patients with disorders of consciousness (DOC). To test these hypotheses, electroencephalographic (EEG) activity at rest was recorded in 12 healthy controls and nine patients with DOC (four vegetative states, and five minimally conscious states). Three-second-lasting EEG epochs centred on each blink instance were analyzed in both time- (BROs) and frequency domains (event-related spectral perturbation or ERSP and intertrial coherence or ITC). Cortical sources of the maximum blink-related delta power, corresponding to the positive peak of the delta BROs, were estimated by standardized Low Resolution Electromagnetic Tomography. In control subjects, as expected, the source of delta BROs was located in the precuneus, whereas in DOC patients, delta BROs were not recognizable and no precuneal localization was possible. Furthermore, we observed a direct relationship between spectral indexes and levels of cognitive functioning in all subjects participating in the study. This reinforces the hypothesis that delta BROs reflect neural processes linked with awareness of the self and of the environment.", "We review the interest of cognitive event-related potentials (ERPs) in comatose, vegetative, or minimally conscious patients. Auditory cognitive ERPs are useful to investigate residual cognitive functions, such as echoic memory (MMN), acoustical and semantic discrimination (P300), and incongruent language detection (N400). While early ERPs (such as the absence of cortical responses on somatosensory-evoked potentials) predict bad outcome, cognitive ERPs (MMN and P300) are indicative of recovery of consciousness. In coma-survivors, cognitive potentials are more frequently obtained when using stimuli that are more ecologic or have an emotional content (such as the patient's own name) than when using classical sine tones." ]
nanoencapsulated triterpenoids from petri dish-cultured	Nanoencapsulated triterpenoids from petri dish-cultured	[ "Biotherapeutic delivery is a rapidly growing field in need of new materials that are easy to modify, are biocompatible, and provide for triggered release of their encapsulated cargo. Herein, we report on a particulate system made of a polysaccharide-based pH-sensitive material that can be efficiently modified to display mannose-based ligands of cell-surface receptors. These ligands are beneficial for antigen delivery, as they enhance internalization and activation of APCs, and are thus capable of modulating immune responses. When compared to unmodified particles or particles modified with a nonspecific sugar residue used in the delivery of antigens to dendritic cells (DCs), the mannosylated particles exhibited enhanced antigen presentation in the context of major histocompatibility complex (MHC) class I molecules. This represents the first demonstration of a mannosylated particulate system that enables enhanced MHC I antigen presentation by DCs in vitro. Our readily functionalized pH-sensitive material may also open new avenues in the development of optimally modulated vaccine delivery systems.", "Nanoparticulate drug/gene carriers have gained much attention in the past decades because of their versatile and tunable properties. However, efficacy of the therapeutic agents can be further enhanced using naturally occurring materials-based nanoparticles. Polysaccharides are an emerging class of biopolymers; therefore, they are generally considered to be safe, non-toxic, biocompatible and biodegradable. Considering that the target of nanoparticle-based therapeutic strategies is localization of biomedical agents in subcellular compartments, a detailed understanding of the cellular mechanism involved in the uptake of polysaccharide-based nanoparticles is essential for safe and efficient therapeutic applications. Uptake of the nanoparticles by the cellular systems occurs with a process known as endocytosis and is influenced by the physicochemical characteristics of nanoparticles such as size, shape and surface chemistry as well as the employed experimental conditions. In this study, we highlight the main endocytosis mechanisms responsible for the cellular uptake of polysaccharide nanoparticles containing drug/gene.", "Acquired drug resistance is becoming common during cancer chemotherapy and leads to treatment failure in clinic. To conquer acquired drug resistance, nanotechnology has been employed to deliver drug. In this paper, we prepared chitosan nanoparticles (CS NPs) capable of entrapping Gefitinib and chloroquine (CQ) for multiple drugs combinational therapy. The results showed that Gefitinib/CQ-NPs were characterized of small particle size about 80.8 ± 9.7 nm and positive zeta potential about 21.3 ± 1.56 mV, and drug controlled to release slowly on a biphasic pattern. Compared with free Gefitinib and Gefitinib loaded NPs, Gefitinib and CQ co-delivery by CS nanoparticles showed the higher inhibition rates and enhanced cell apoptosis. Through western blot analysis, we found that Gefitinib could promote LC3 expression, which is the marker of autophagosomes. So, the acquired drug resistance may be associated with autophagy. CQ as an inhibitor of autophagolysosomes formation could overcome autophagy in the resistant cells. These findings demonstrated that chitosan nanoparticles entrapping Gefitinib and chloroquine have the potential to overcome acquired resistance and improve cancer treatment efficacy, especially towards resistant strains. Graphical abstract: Cellular distribution of NPs after incubating QGY (a) and QGY/Gefitinib cells (b) with rhodamine B-labeled NPs.", "Nanoparticles (NPs) are of similar size to typical cellular components and proteins, and can efficiently intrude living cells. A detailed understanding of the involved processes at the molecular level is important for developing NPs designed for selective uptake by specific cells, for example, for targeted drug delivery. In addition, this knowledge can greatly assist in the engineering of NPs that should not penetrate cells so as to avoid adverse health effects. In recent years, a wide variety of experiments have been performed to elucidate the mechanisms underlying cellular NP uptake. Here, we review some select recent studies, which are often based on fluorescence microscopy and sophisticated strategies for specific labelling of key cellular components. We address the role of the protein corona forming around NPs in biological environments, and describe recent work revealing active endocytosis mechanisms and pathways involved in their cellular uptake. Passive uptake is also discussed. The current state of knowledge is summarized, and we point to issues that still need to be addressed to further advance our understanding of cellular NP uptake.", "We investigate the effect of antidiabetic Momordica charantia fruit juice on T cells' differentiation, through plasmatic cytokine quantification in type 1 diabetic rats (T1D). Male Wistar rats were rendered diabetic by the injection of five low doses of streptozotocin. Then, animals were treated with Momordica charantia fruit juice for 28 consecutive days. Plasmatic levels of Th1 interleukin- (IL-) 02 and interferon- (IFN-) γ, Th2 (IL-4), and regulatory (IL-10) cytokines were determined in rats. We observed that fruit juice induced a significant decrease in blood glucose of T1D rats. Besides, the concentrations of IL-2 and IFN-γ significantly increased while those of IL-4 and IL-10 diminished in diabetic rats compared to control animals. Interestingly, after treatment with Momordica charantia fruit juice, IL-4 and IL-10 levels significantly increased in diabetic rats, while IL-2 and IFN-γ concentrations decreased, suggesting a Th2 phenotype in these animals. Phytochemical analysis of the fruit juice revealed the presence of tannins, flavonoids, and coumarins, compounds which possess antioxidant activity. This study shows that Momordica charantia fruit juice, by lowering the hyperglycemia, induced a shift of proinflammatory Th1 phenotype in T1D rats towards a favorable anti-inflammatory Th2 status. These effects might be due to the presence of antioxidant compounds in the juice and confirms the use of this plant in the treatment of autoimmune type 1 diabetes.", "Ursolic, oleanolic and betulinic acids are representative pentacyclic triterpenoids found in various plants and fruits. Despite having marked antitumor potentials, the very poor water solubility of these triterpenes hinders treatment development. Nanotechnology can enhance solubility, stability, bioavailability and phytochemical delivery, improving the therapeutic efficiency of triterpenes. This review focuses on the formulation, characterization and in vitro/in vivo evaluation of several delivery nanosystems used to enhance the physicochemical properties of ursolic, oleanolic and betulinic acids.", "Insulin resistance has been associated with metabolic and hemodynamic alterations and higher cardio metabolic risk. There is great variability in the threshold homeostasis model assessment of insulin resistance (HOMA-IR) levels to define insulin resistance. The purpose of this study was to describe the influence of age and gender in the estimation of HOMA-IR optimal cut-off values to identify subjects with higher cardio metabolic risk in a general adult population. It included 2459 adults (range 20-92 years, 58.4% women) in a random Spanish population sample. As an accurate indicator of cardio metabolic risk, Metabolic Syndrome (MetS), both by International Diabetes Federation criteria and by Adult Treatment Panel III criteria, were used. The effect of age was analyzed in individuals with and without diabetes mellitus separately. ROC regression methodology was used to evaluate the effect of age on HOMA-IR performance in classifying cardio metabolic risk. In Spanish population the threshold value of HOMA-IR drops from 3.46 using 90th percentile criteria to 2.05 taking into account of MetS components. In non-diabetic women, but no in men, we found a significant non-linear effect of age on the accuracy of HOMA-IR. In non-diabetic men, the cut-off values were 1.85. All values are between 70th-75th percentiles of HOMA-IR levels in adult Spanish population. The consideration of the cardio metabolic risk to establish the cut-off points of HOMA-IR, to define insulin resistance instead of using a percentile of the population distribution, would increase its clinical utility in identifying those patients in whom the presence of multiple metabolic risk factors imparts an increased metabolic and cardiovascular risk. The threshold levels must be modified by age in non-diabetic women." ]

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